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GitLab

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<h3>

Steffen Möller pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/atropos/commit/276ab63265f17afe9eed3a1e838da8d996f04168">276ab632</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2019-11-21T15:03:19Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.22+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/atropos/commit/19ac140614f777bcdf8e147ec0b7ffc4d74954b7">19ac1406</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2019-11-21T15:09:00Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.22+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/atropos/commit/97f343a54c799c5423506527f547751870b9d5a6">97f343a5</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2019-11-21T15:16:29Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.22+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/atropos/commit/dbfa561b04043199fbaf24ea48f33f0e88285651">dbfa561b</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2019-11-21T15:24:31Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.22+dfsg</pre>

</li>

</ul>

<h4>10 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">

CHANGES.md

</a>

</li>

<li class="file-stats">

<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

Makefile

</a>

</li>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#e14d2613b23186c0c8a0c4d5d16951517ef1d5af">

atropos/_version.py

</a>

</li>

<li class="file-stats">

<a href="#fbbf6d960c8a09ddcb61bf36ff75c30c2ae6fe6b">

atropos/align/__init__.py

</a>

</li>

<li class="file-stats">

<a href="#654374a170d9d9959f276c28f2cf60cb908a7d25">

atropos/commands/detect/__init__.py

</a>

</li>

<li class="file-stats">

<a href="#df0576cbb783bc50b36e1efa3cbe0564a26c8295">

doc/conf.py

</a>

</li>

<li class="file-stats">

<a href="#ee1d7278a009e2c5c652622fe43dc77e39af740d">

doc/guide.rst

</a>

</li>

<li class="file-stats">

<a href="#1bbcd8980c541f52998ccf56da078edd2ca6a2d0">

doc/index.rst

</a>

</li>

<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>

<hr>

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1

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

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Changes</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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<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_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="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">

3

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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"><span class="gh" style="color: #999;">v1.1.22 (dev)</span></span>

</pre>

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<td class="diff-line-num new old_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="diff-line-num new new_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">

4

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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="LC4" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------</span></span>

</pre>

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

5

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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="LC5" class="line" lang="markdown"><span class="p">*</span> Documentation fixes (#79)</span>

</pre>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">*</span> Fix for index error when running <span class="sb" style="color: #d14;">`detect`</span> command (#80)</span>

</pre>

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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="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="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 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="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">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"><span class="gh" style="color: #999;">v1.1.21 (2018.11.24)</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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<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

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<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 class="gh" style="color: #999;">--------------------</span></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="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">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="p">*</span> Added long options for paired adapter parameters.</span>

</pre>

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</table>

<br>

</li>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</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="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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,8 +19,7 @@ test:</td>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="make">  <span class="nv" style="color: #008080;">$(TEST)</span></span>

</pre>

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

</pre>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"><span class="nl">docs</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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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="LC22" class="line" lang="make">  make <span class="nt" style="color: #000080;">-C</span> docs api</span>

</pre>

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

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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="LC23" class="line" lang="make">  make <span class="nt" style="color: #000080;">-C</span> docs html</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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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="LC22" class="line" lang="make">  make <span class="nt" style="color: #000080;">-C</span> doc html</span>

</pre>

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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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="make"><span class="nl">readme</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

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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">

26

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

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make">  pandoc <span class="nt" style="color: #000080;">--from</span><span class="o" style="font-weight: 600;">=</span>markdown <span class="nt" style="color: #000080;">--to</span><span class="o" style="font-weight: 600;">=</span>rst <span class="nt" style="color: #000080;">--output</span><span class="o" style="font-weight: 600;">=</span>README.rst README.md</span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -58,7 +57,7 @@ release:</td>

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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="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="make">  <span class="nv" style="color: #008080;">$(TEST)</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">

59

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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="make">  python setup.py sdist bdist_wheel</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

60

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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">

59

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

<pre style="margin: 0;"> <span id="LC59" class="line" lang="make">  <span class="c" style="color: #998; font-style: italic;"># release</span></span>

</pre>

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

61

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<td class="diff-line-num new_line old" data-linenumber="60" 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="LC61" class="line" lang="make">  python setup.py sdist upload</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="62" style="width: 35px; color: rgba(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="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="make">  python setup.py sdist upload<span class="idiff left"> </span><span class="nt" style="color: #000080;"><span class="idiff">-r</span></span><span class="idiff right"> pypi</span></span>

</pre>

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<td class="diff-line-num 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">

62

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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">

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

<pre style="margin: 0;"> <span id="LC61" class="line" lang="make">  git push origin <span class="nt" style="color: #000080;">--tags</span></span>

</pre>

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<td class="diff-line-num old_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">

63

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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="make">  <span class="nv" style="color: #008080;">$(github_release)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

64

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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="make">  <span class="nv" style="color: #008080;">$(docker)</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#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 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

</td>

<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">

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![Travis CI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/jdidion/atropos.svg?branch=<span class="idiff left">master</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.org/jdidion/atropos]</span>)</span>

</pre>

</td>

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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">

</td>

<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="p">[</span><span class="nv" style="color: #008080;">![Travis CI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://travis-ci.org/jdidion/atropos.svg?branch=<span class="idiff left">1.1</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff right">](https://travis-ci.org/jdidion/atropos</span>)</span>

</pre>

</td>

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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 class="p">[</span><span class="nv" style="color: #008080;">![PyPi</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/pypi/v/atropos.svg</span><span class="p">)</span>](https://pypi.python.org/pypi/atropos)</span>

</pre>

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![DOI</span><span class="p">](</span><span class="sx" style="color: #d14;">https://zenodo.org/badge/61393086.svg</span><span class="p">)</span>](https://zenodo.org/badge/latestdoi/61393086)</span>

</pre>

</td>

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

<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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<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>

</td>

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<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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,7 +88,7 @@ Please cite as:</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="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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<pre style="margin: 0;"> <span id="LC88" class="line" lang="markdown">The results in the paper can be fully reproduced using the workflow defined in the <span class="p">[</span><span class="nv" style="color: #008080;">paper</span><span class="p">](</span><span class="sx" style="color: #d14;">paper/README.md</span><span class="p">)</span> directory.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown">The citation for the original Cutadapt paper is:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="markdown"><span class="gt" style="color: #a00;"><span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown"><span class="gt" style="color: #a00;">> Marcel Martin. "Cutadapt removes adapter sequences from high-throughput sequencing reads." EMBnet.Journal, 17(1):10-12, May 2011. http://dx.doi.org/10.14806/ej.17.1.200</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" style="width: 35px; color: rgba(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">@@ -127,12 +127,15 @@ The citation for the original Cutadapt paper is:</td>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"><span class="p">*</span> Provide option for RNA-seq data that will trim polyA sequence.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="markdown"><span class="p">*</span> Add formal config file support (#53)</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="129" style="width: 35px; color: rgba(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="LC129" class="line" lang="markdown"><span class="p">*</span> Automate crash reporting using <span class="p">[</span><span class="nv" style="color: #008080;">sentry</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/getsentry/raven-python</span><span class="p">)</span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="markdown"><span class="p">*</span> Look at <span class="p">[</span><span class="nv" style="color: #008080;">NGMerge</span><span class="p">]</span> for improving read merging: https://github.com/harvardinformatics/NGmerge</span>

</pre>

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<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">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="markdown"><span class="p">*</span> Look at replacing pysam with <span class="p">[</span><span class="nv" style="color: #008080;">pybam</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/JohnLonginotto/pybam</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 1.4</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="markdown"><span class="p">*</span> Currently, InsertAligner requires a single 3' adapter for each end. Adapter trimming will later be generalized so that A) the InsertAligner can handle multiple matched pairs of adapters and/or B) multiple different aligners can be used for different adapters.</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="136" style="width: 35px; color: rgba(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="LC136" class="line" lang="markdown"><span class="p">*</span> Integrate with <span class="p">[</span><span class="nv" style="color: #008080;">AdapterBase</span><span class="p">](</span><span class="sx" style="color: #d14;">https://github.com/NCBI-Hackathons/OnlineAdapterDatabase</span><span class="p">)</span> for improved matching of detected contaminants to known adapters, automated trimming of datasets with known adapters, and (opt-in) submission of adapter information for novel datasets.</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="137" style="width: 35px; color: rgba(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="LC137" class="line" lang="markdown"><span class="p">*</span> Migrate to seqio (https://github.com/jdidion/seqio) for reading/writing sequence files.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(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="LC138" class="line" lang="markdown"><span class="p">    *</span> Also look at using HTSeq instead: https://github.com/simon-anders/htseq</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="136" style="width: 35px; color: rgba(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="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="markdown"><span class="p">*</span> General-purpose read filtering based on read ID: https://github.com/marcelm/cutadapt/issues/107.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

137

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

140

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="markdown"><span class="p">*</span> Currently, SAM/BAM input files must be name sorted; add an option to 1) pre-sort reads inline using samtools or sambamba, or 2) cache each read in memory until its mate is found.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

138

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

141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="169" style="width: 35px; color: rgba(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="172" style="width: 35px; color: rgba(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">@@ -169,8 +172,10 @@ The citation for the original Cutadapt paper is:</td>

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169

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### 2.0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="170" style="width: 35px; color: rgba(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="173" style="width: 35px; color: rgba(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="LC173" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="171" style="width: 35px; color: rgba(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="174" style="width: 35px; color: rgba(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="LC174" class="line" lang="markdown"><span class="p">*</span> Simplification of command line options, perhaps by further splitting functionality up into different sub-commands, but also by more intelligent choices for default option values based on context.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="172" style="width: 35px; color: rgba(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="175" style="width: 35px; color: rgba(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="LC175" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="172" style="width: 35px; color: rgba(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="176" style="width: 35px; color: rgba(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="LC176" class="line" lang="markdown"><span class="p">*</span> Consider adding additional report formats</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="173" 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">

173

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<td class="diff-line-num new_line old" data-linenumber="177" 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="LC173" class="line" lang="markdown"><span class="p">    *</span> https://github.com/marcelm/cutadapt/issues/112</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="174" style="width: 35px; color: rgba(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="177" style="width: 35px; color: rgba(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="LC177" class="line" lang="markdown"><span class="p">*</span> Add fuzzy matching: https://github.com/Daniel-Liu-c0deb0t/Java-Fuzzy-Search</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="174" style="width: 35px; color: rgba(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="178" style="width: 35px; color: rgba(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="LC178" class="line" lang="markdown"><span class="p">*</span> https://github.com/marcelm/cutadapt/issues/112</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="174" style="width: 35px; color: rgba(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="179" style="width: 35px; color: rgba(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="LC179" class="line" lang="markdown"><span class="p">*</span> Performance enhancements using</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(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="180" style="width: 35px; color: rgba(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="LC180" class="line" lang="markdown"><span class="p">    *</span> http://numba.pydata.org/</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(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="181" style="width: 35px; color: rgba(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="LC181" class="line" lang="markdown"><span class="p">    *</span> https://github.com/undefx/vecpy</span>

</pre>

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<br>

</li>

<li id="e14d2613b23186c0c8a0c4d5d16951517ef1d5af">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#e14d2613b23186c0c8a0c4d5d16951517ef1d5af"><strong>atropos/_version.py</strong></a>

<hr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -23,8 +23,8 @@ def get_keywords():</td>

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

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

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># setup.py/versioneer.py will grep for the variable names, so they must</span></span>

</pre>

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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="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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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># each be defined on a line of their own. _version.py will just call</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># get_keywords().</span></span>

</pre>

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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">

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

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python">    <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (tag: 1.1.2<span class="idiff left right">1</span>)"</span></span>

</pre>

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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">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python">    <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">1b7273b082551e80652a45df2736e5ffff8ce7f9</span>"</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">    <span class="n" style="color: #333;">git_refnames</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">" (tag: 1.1.2<span class="idiff left right">2</span>)"</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">    <span class="n" style="color: #333;">git_full</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"<span class="idiff left right">2b15c778f0ccf1d0fb753e4334fa6dc0048a9ee6</span>"</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">    <span class="n" style="color: #333;">keywords</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"refnames"</span><span class="p">:</span> <span class="n" style="color: #333;">git_refnames</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">:</span> <span class="n" style="color: #333;">git_full</span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">keywords</span></span>

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

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<li id="fbbf6d960c8a09ddcb61bf36ff75c30c2ae6fe6b">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#fbbf6d960c8a09ddcb61bf36ff75c30c2ae6fe6b"><strong>atropos/align/__init__.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(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="212" style="width: 35px; color: rgba(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">@@ -212,6 +212,12 @@ MatchInfo = namedtuple("MatchInfo", (</td>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># * http://www.combio.pl/alfree/tools/</span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># * http://www.combio.pl/alfree</span></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># * http://bioinformatics.org.au/tools/decaf+py/</span></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 12. https://github.com/sdu-hpcl/BGSA</span></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 13. Train a NN to approximate the pairwise alignment distance</span></span>

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<pre style="margin: 0;">+<span id="LC217" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># https://academic.oup.com/bioinformatics/advance-article-abstract/doi/10.1093/bioinformatics/bty887/5140215?redirectedFrom=fulltext</span></span>

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

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<pre style="margin: 0;">+<span id="LC218" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 14. Nucl2vec: https://github.com/prakharg24/Nucl2vec (local alignment only - could</span></span>

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<td class="diff-line-num new old_line" data-linenumber="215" style="width: 35px; color: rgba(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="219" style="width: 35px; color: rgba(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="LC219" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># it be adapted to semi-global?)</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="220" style="width: 35px; color: rgba(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="LC220" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># * Can re-implement in SpaCy? https://spacy.io/usage/vectors-similarity</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">InsertAligner</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python">    <span class="s" style="color: #d14;">"""Implementation of an insert matching algorithm.</span></span>

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<br>

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<li id="654374a170d9d9959f276c28f2cf60cb908a7d25">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#654374a170d9d9959f276c28f2cf60cb908a7d25"><strong>atropos/commands/detect/__init__.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">@@ -8,7 +8,7 @@ from atropos.align import Aligner, SEMIGLOBAL</td>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">atropos.commands.base</span> <span class="kn" style="font-weight: 600;">import</span> <span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python">    <span class="n" style="color: #333;">BaseCommandRunner</span><span class="p">,</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">,</span> <span class="n" style="color: #333;">SingleEndPipelineMixin</span><span class="p">,</span> <span class="n" style="color: #333;">PairedEndPipelineMixin</span><span class="p">)</span></span>

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python">    <span class="n" style="color: #333;">reverse_complement</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_complexity</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left">enumerate_range</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">run_interruptible</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python">    <span class="n" style="color: #333;">reverse_complement</span><span class="p">,</span> <span class="n" style="color: #333;">sequence_complexity</span><span class="p">,</span> <span class="n" style="color: #333;">run_interruptible</span><span class="p">)</span></span>

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

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># TODO: Test whether using rc=True in parse_known_contaminants is as fast</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># and as accurate as testing both the forward and reverse complement</span></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># strategy is to use CountTable and, upon each kmer addition, test whether its</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># count exceeds some threshold (perhaps by maintaining a running distribution of</span></span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># all kmer counts). These high-abundance kmers could then be profiled using a</span></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># second pass. Another strategy is to compute summary metrics for reads based on<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># kmer abundance, as per<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># second pass. Another strategy is to compute summary metrics for reads based on</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># kmer abundance, as per</span></span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># http://khmer-recipes.readthedocs.io/en/latest/001-extract-reads-by-coverage/index.html</span></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Then take reads in the furthest-right peak and extract common sequences from</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># those.</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -51,7 +51,7 @@ class CommandRunner(BaseCommandRunner):</td>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></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="python"><span class="s" style="color: #d14;">    """</span></span>

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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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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">    <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'detect'</span></span>

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<td class="diff-line-num new_line old" data-linenumber="54" 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="LC54" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" style="width: 35px; color: rgba(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="LC54" class="line" lang="python"></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">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__call__</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 old_line" data-linenumber="56" style="width: 35px; color: rgba(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="56" style="width: 35px; color: rgba(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="LC56" class="line" lang="python">        <span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span> <span class="ow" style="font-weight: 600;">or</span> <span class="mi" style="color: #099;">12</span></span>

</pre>

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<td class="diff-line-num old_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="n" style="color: #333;">n_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">max_reads</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="60" style="width: 35px; color: rgba(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="60" style="width: 35px; color: rgba(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">@@ -60,7 +60,7 @@ class CommandRunner(BaseCommandRunner):</td>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(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="LC60" class="line" lang="python">        <span class="n" style="color: #333;">known_contaminants</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">include</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'unknown'</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python">            <span class="n" style="color: #333;">known_contaminants</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">load_known_adapters</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="63" 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="LC63" class="line" lang="python"><span class="idiff left right">        </span></span>

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<td class="diff-line-num new old_line" data-linenumber="64" style="width: 35px; color: rgba(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="LC63" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(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="LC64" class="line" lang="python">        <span class="n" style="color: #333;">detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">detector</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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC65" 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;">detector</span><span class="p">:</span></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">

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">known_contaminants</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">include</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'known'</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -69,9 +69,9 @@ class CommandRunner(BaseCommandRunner):</td>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python">                <span class="n" style="color: #333;">detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'heuristic'</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="71" style="width: 35px; color: rgba(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="LC71" class="line" lang="python">                <span class="n" style="color: #333;">detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'khmer'</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="python"><span class="idiff left right">        </span></span>

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<td class="diff-line-num new old_line" data-linenumber="73" style="width: 35px; color: rgba(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="LC72" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">        <span class="n" style="color: #333;">detector_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="n" style="color: #333;">known_contaminants</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">known_contaminants</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="python"><span class="idiff left right">            </span></span>

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<td class="diff-line-num new old_line" data-linenumber="75" style="width: 35px; color: rgba(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="LC74" class="line" lang="python"></span>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">detector</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'known'</span><span class="p">:</span></span>

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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="python">            <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</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;">"Detecting contaminants using the known-only algorithm"</span><span class="p">)</span></span>

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<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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -88,34 +88,37 @@ class CommandRunner(BaseCommandRunner):</td>

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python">            <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python">                <span class="s" style="color: #d14;">"Detecting contaminants using the kmer-based algorithm"</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;">detector_class</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">KhmerDetector</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python">        </span>

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<td class="diff-line-num new old_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="LC91" 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 old_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="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span><span class="s" style="color: #d14;">"Invalid value for 'detector': {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">detector</span><span class="p">))</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>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python">        <span class="n" style="color: #333;">summary_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" 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="95" 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="LC93" class="line" lang="python">            <span class="n" style="color: #333;">kmer_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kmer_size</span><span class="p">,</span> <span class="n" style="color: #333;">n_reads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">n_reads</span><span class="p">,</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_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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<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;">kmer_size</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">kmer_size</span><span class="p">,</span> <span class="n" style="color: #333;">n_reads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">n_reads</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_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="n" style="color: #333;">overrep_cutoff</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">overrep_cutoff</span><span class="p">,</span> <span class="n" style="color: #333;">include</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">include</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_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;">past_end_bases</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">past_end_bases</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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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(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="LC98" class="line" lang="python">        <span class="n" style="color: #333;">detector_args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">summary_args</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="99" 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="LC97" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

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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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(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="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;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">paired</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_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">

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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">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python">            <span class="n" style="color: #333;">detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">PairedDetector</span><span class="p">(</span><span class="n" style="color: #333;">detector_class</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">detector_args</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(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="LC102" 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 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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<td class="diff-line-num new_line" data-linenumber="103" style="width: 35px; color: rgba(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="LC103" class="line" lang="python">            <span class="n" style="color: #333;">detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">detector_class</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">detector_args</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="python"><span class="idiff left right">        </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="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'detect'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">summary_args</span></span>

</pre>

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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">

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

</pre>

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<td class="diff-line-num 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">

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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">

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'detect'</span><span class="p">][</span><span class="s" style="color: #d14;">'known_contaminants'</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="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">

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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">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">                <span class="n" style="color: #333;">known_contaminants</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summarize</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" 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="LC107" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python">        <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="python">            <span class="s" style="color: #d14;">"Detecting adapters and other potential contaminant "</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python">            <span class="s" style="color: #d14;">"sequences based on </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d-mers in </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d reads"</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_size</span><span class="p">,</span> <span class="n" style="color: #333;">n_reads</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># currently only single-threaded operation is supproted</span></span>

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">summary</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">mode</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'serial'</span><span class="p">,</span> <span class="n" style="color: #333;">threads</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">run_interruptible</span><span class="p">(</span><span class="n" style="color: #333;">detector</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">raise_on_error</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="LC117" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Match</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python">    <span class="s" style="color: #d14;">"""A contaminant match.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC121" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python"><span class="s" style="color: #d14;">        seq_or_contam: The matched sequence.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;">        count: The number of matches.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" style="width: 35px; color: rgba(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="146" style="width: 35px; color: rgba(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">@@ -143,34 +146,34 @@ class Match(object):</td>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longest_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="144" style="width: 35px; color: rgba(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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147

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">reads</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="145" style="width: 35px; color: rgba(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="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

148

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_longest_match</span><span class="p">(</span><span class="n" style="color: #333;">reads</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="149" 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="LC146" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="147" style="width: 35px; color: rgba(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="149" style="width: 35px; color: rgba(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="LC149" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="147" style="width: 35px; color: rgba(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="150" style="width: 35px; color: rgba(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="LC150" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__len__</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 old_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

151

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="152" 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="LC149" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="150" style="width: 35px; color: rgba(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="152" style="width: 35px; color: rgba(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="LC152" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(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="153" style="width: 35px; color: rgba(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="LC153" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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 old_line" data-linenumber="151" style="width: 35px; color: rgba(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="154" style="width: 35px; color: rgba(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="LC154" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_known</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="152" style="width: 35px; color: rgba(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="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

155

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="s" style="color: #d14;">"{} => {} ({}))"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="153" style="width: 35px; color: rgba(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="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

156

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">known_seqs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="154" style="width: 35px; color: rgba(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="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

157

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<pre style="margin: 0;"> <span id="LC157" 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 old_line" data-linenumber="155" style="width: 35px; color: rgba(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="158" style="width: 35px; color: rgba(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="LC158" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="156" 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">

156

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<td class="diff-line-num new_line old" data-linenumber="159" 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="LC156" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(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="159" style="width: 35px; color: rgba(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="LC159" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(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="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

160

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(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="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

161

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">seq_complexity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="python">        <span class="s" style="color: #d14;">"""The complexity of the sequence (0=homopolymer, 2=random).</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">sequence_complexity</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">count_is_frequency</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python">        <span class="s" style="color: #d14;">"""Whether `self.count` represents a frequency.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_contaminant</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">contam</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python">        <span class="s" style="color: #d14;">"""Set the known contaminant from a :class:`ContaminantMatcher`.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_known</span><span class="p">(</span><span class="n" style="color: #333;">contam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="p">[</span><span class="n" style="color: #333;">contam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">],</span> <span class="n" style="color: #333;">match_frac</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_known</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python">        <span class="s" style="color: #d14;">"""Set the known contaminant.</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="178" style="width: 35px; color: rgba(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="181" style="width: 35px; color: rgba(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">@@ -178,13 +181,13 @@ class Match(object):</td>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">known_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqs</span></span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_frac</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match_frac</span></span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_frac2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match_frac2</span></span>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC184" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_known</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python">        <span class="s" style="color: #d14;">"""Whether the matching sequence is a known contaminant.</span></span>

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">known_seqs</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_longest_match</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">sequences</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">        <span class="s" style="color: #d14;">"""Set the longest matching sequence from a set of sequences.</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="193" style="width: 35px; color: rgba(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="196" style="width: 35px; color: rgba(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">@@ -193,7 +196,7 @@ class Match(object):</td>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">            <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">idx</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longest_match</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longest_match</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">seqlen</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longest_match</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">:],</span> <span class="n" style="color: #333;">seqlen</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"><span class="idiff left right">    </span></span>

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

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">estimate_abundance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">read_sequences</span><span class="p">):</span></span>

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

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python">        <span class="s" style="color: #d14;">"""Determine whether this match's sequence is within 'seq' by simple</span></span>

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<td class="diff-line-num new_line" data-linenumber="202" style="width: 35px; color: rgba(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="LC202" class="line" lang="python"><span class="s" style="color: #d14;">        exact string comparison.</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="204" style="width: 35px; color: rgba(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">@@ -201,7 +204,7 @@ class Match(object):</td>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abundance</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python">            <span class="mi" style="color: #099;">1</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read_seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read_sequences</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">read_seq</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="207" 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="LC204" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC207" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">summarize</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python">        <span class="n" style="color: #333;">summary</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

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<td class="diff-line-num new_line" data-linenumber="210" style="width: 35px; color: rgba(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="LC210" class="line" lang="python">            <span class="n" style="color: #333;">longest_kmer</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" style="width: 35px; color: rgba(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="227" style="width: 35px; color: rgba(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">@@ -224,9 +227,10 @@ class Match(object):</td>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python">                <span class="n" style="color: #333;">known_seqs</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">known_seqs</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">summary</span></span>

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

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">ContaminantMatcher</span><span class="p">(</span><span class="nb" style="color: #0086b3;">object</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python">    <span class="s" style="color: #d14;">"""Matches a known contaminant against other sequences.</span></span>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC235" class="line" lang="python"><span class="s" style="color: #d14;">        seq: The contaminant sequence.</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;">        names: Sequence of names for the contaminant.</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -241,14 +245,14 @@ class ContaminantMatcher(object):</td>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmers</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kmer_size</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</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="LC244" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">match</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqrc</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns (num_matches, num_contam_kmers, num_seq_kmers).</span></span>

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<pre style="margin: 0;">-<span id="LC247" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">        </span></span></span>

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

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"><span class="s" style="color: #d14;">        Args:</span></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"><span class="s" style="color: #d14;">            seq: The sequence to match.</span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"><span class="s" style="color: #d14;">            seqrc: The reverse complement of `seq`.</span></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">        </span></span></span>

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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"></span>

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

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"><span class="s" style="color: #d14;">            Tuple (f1, f2, seq), where f1 is the fraction of contaminant kmers</span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"><span class="s" style="color: #d14;">            that match, f2 is the fraction of sequence kmers that match, and</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -258,12 +262,12 @@ class ContaminantMatcher(object):</td>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python">            <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python">        <span class="n" style="color: #333;">fw_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmers</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fw_kmers</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="python"><span class="idiff left right">        </span></span>

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

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">        <span class="n" style="color: #333;">rv_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python">            <span class="n" style="color: #333;">seqrc</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seqrc</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python">        <span class="n" style="color: #333;">rv_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmers</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">rv_kmers</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC266" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC270" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fw_matches</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">rv_matches</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python">            <span class="n" style="color: #333;">n_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fw_matches</span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="python">            <span class="n" style="color: #333;">kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fw_kmers</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -272,22 +276,23 @@ class ContaminantMatcher(object):</td>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python">            <span class="n" style="color: #333;">n_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rv_matches</span></span>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python">            <span class="n" style="color: #333;">kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">rv_kmers</span></span>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python">            <span class="n" style="color: #333;">compare_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqrc</span></span>

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC279" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC280" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">n_matches</span></span>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python">        <span class="n" style="color: #333;">match_frac1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match_frac2</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="LC282" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_kmers</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python">            <span class="n" style="color: #333;">match_frac1</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_matches</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_kmers</span></span>

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<pre style="margin: 0;"> <span id="LC284" 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;">kmers</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python">            <span class="n" style="color: #333;">match_frac2</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_matches</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;">kmers</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">match_frac1</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="p">,</span> <span class="n" style="color: #333;">compare_seq</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC286" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">match_frac1</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="p">,</span> <span class="n" style="color: #333;">compare_seq</span></span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">create_contaminant_matchers</span><span class="p">(</span><span class="n" style="color: #333;">contaminants</span><span class="p">,</span> <span class="n" style="color: #333;">kmer_size</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python">    <span class="s" style="color: #d14;">"""Create :class:`ContaminantMatcher`s from sequences.</span></span>

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<pre style="margin: 0;">-<span id="LC286" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC291" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python"><span class="s" style="color: #d14;">        contaminants: A dict of {seq:names}.</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python"><span class="s" style="color: #d14;">        kmer_size: The kmer size.</span></span>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python"><span class="s" style="color: #d14;">        A list of :class:`ContaminantMatcher`s.</span></span>

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

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -296,19 +301,20 @@ def create_contaminant_matchers(contaminants, kmer_size):</td>

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<pre style="margin: 0;"> <span id="LC301" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">names</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contaminants</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iter_sequences</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python">    <span class="p">]</span></span>

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

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<pre style="margin: 0;">+<span id="LC304" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Detector</span><span class="p">(</span><span class="n" style="color: #333;">SingleEndPipelineMixin</span><span class="p">,</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC306" class="line" lang="python">    <span class="s" style="color: #d14;">"""Base class for contaminant detectors.</span></span>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></span></span>

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

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

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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"><span class="s" style="color: #d14;">        kmer_size: Size of kmers to match.</span></span>

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<pre style="margin: 0;"> <span id="LC310" class="line" lang="python"><span class="s" style="color: #d14;">        n_reads: Number of reads to sample.</span></span>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python"><span class="s" style="color: #d14;">        overrep_cutoff: Degree of overrepresentation required for a kmer to be</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python"><span class="s" style="color: #d14;">            considered as a contaminant.</span></span>

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<pre style="margin: 0;">-<span id="LC307" class="line" lang="python"><span class="s" style="color: #d14;">        known_contaminant: :class:`ContaminantMatcher`s to match against.</span></span>

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<pre style="margin: 0;">+<span id="LC313" class="line" lang="python"><span class="s" style="color: #d14;">        known_contaminant<span class="idiff left right">s</span>: :class:`ContaminantMatcher`s to match against.</span></span>

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="python"><span class="s" style="color: #d14;">        past_end_bases: On Illumina, long runs of A (and sometimes other bases)</span></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python"><span class="s" style="color: #d14;">            can signify that the sequencer has read past the end of a fragment</span></span>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="python"><span class="s" style="color: #d14;">            that is shorter than the read length + adapter length. Those</span></span>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="python"><span class="s" style="color: #d14;">            bases will be removed from any sequencers before looking for<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="python"><span class="s" style="color: #d14;">            bases will be removed from any sequencers before looking for</span></span>

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<pre style="margin: 0;"> <span id="LC318" class="line" lang="python"><span class="s" style="color: #d14;">            matching contaminants.</span></span>

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

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -329,32 +335,32 @@ class Detector(SingleEndPipelineMixin, Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_past_end_regexp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="n" style="color: #333;">past_end_bases</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_past_end_regexp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">re</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">compile</span><span class="p">(</span><span class="s" style="color: #d14;">'|'</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="python">                    <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'{8,}.*|'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'{2,}$'</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC338" class="line" lang="python">                    <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'{8,}.*|'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'{2,}$'</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="339" style="width: 35px; color: rgba(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="LC339" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">base</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">past_end_bases</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC340" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">min_report_freq</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="python">        <span class="s" style="color: #d14;">"""The minimum contaminant frequency required for a contaminant to be</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python"><span class="s" style="color: #d14;">        reported.</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">NotImplementedError</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC347" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="342" style="width: 35px; color: rgba(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="348" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">set_read_length</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">record</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="349" style="width: 35px; color: rgba(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="LC349" class="line" lang="python">        <span class="k" style="font-weight: 600;">assert</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_length</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="344" style="width: 35px; color: rgba(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="350" style="width: 35px; color: rgba(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="LC350" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_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;">record</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="351" 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="LC345" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="346" style="width: 35px; color: rgba(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="LC351" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="346" style="width: 35px; color: rgba(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="LC352" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">handle_records</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">context</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">context</span><span class="p">[</span><span class="s" style="color: #d14;">'size'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_length</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_read_length</span><span class="p">(</span><span class="n" style="color: #333;">records</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handle_records</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">)</span></span>

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

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<pre style="margin: 0;">+<span id="LC358" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">handle_reads</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">context</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</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="LC360" class="line" lang="python">        <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filter_seq</span><span class="p">(</span><span class="n" style="color: #333;">read1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC362" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_sequences</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC357" class="line" lang="python"><span class="idiff left right">    </span></span>

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

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<pre style="margin: 0;">+<span id="LC363" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="364" style="width: 35px; color: rgba(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="LC364" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_filter_seq</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sequence_complexity</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mf" style="color: #099;">1.0</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC366" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="365" style="width: 35px; color: rgba(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="371" style="width: 35px; color: rgba(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">@@ -365,19 +371,19 @@ class Detector(SingleEndPipelineMixin, Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span><span class="p">:</span></span>

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372

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<pre style="margin: 0;"> <span id="LC372" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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367

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373

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="368" 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">

368

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<td class="diff-line-num new_line old" data-linenumber="374" 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="LC368" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="369" style="width: 35px; color: rgba(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="374" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

374

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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="LC374" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="369" style="width: 35px; color: rgba(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="LC375" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">matches</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

370

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns the current set of matches.</span></span>

</pre>

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371

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

372

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<td class="diff-line-num new_line" data-linenumber="378" style="width: 35px; color: rgba(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="LC378" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_matches</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span> <span class="ow" style="font-weight: 600;">or</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

373

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<td class="diff-line-num new_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

379

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filter_and_sort</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

</pre>

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374

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<td class="diff-line-num new_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

380

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_matches</span></span>

</pre>

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375

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<td class="diff-line-num new_line old" data-linenumber="381" 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="LC375" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="376" style="width: 35px; color: rgba(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="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

381

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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="LC381" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="376" style="width: 35px; color: rgba(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="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

382

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<pre style="margin: 0;"> <span id="LC382" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_filter_and_sort</span><span class="p">(</span></span>

</pre>

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377

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<td class="diff-line-num new_line old" data-linenumber="383" 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="LC377" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">min_len</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_complexity</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.1</span><span class="p">,</span> <span class="n" style="color: #333;">min_match_frac</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span><span class="idiff left right"> </span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="383" style="width: 35px; color: rgba(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="LC383" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">min_len</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_complexity</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">1.1</span><span class="p">,</span> <span class="n" style="color: #333;">min_match_frac</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.1</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

378

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<td class="diff-line-num new_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

384

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

<pre style="margin: 0;"> <span id="LC384" class="line" lang="python">            <span class="n" style="color: #333;">limit</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">20</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

385

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="python">        <span class="s" style="color: #d14;">"""Identify, filter, and sort contaminants.</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="386" 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="LC380" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">        </span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="386" style="width: 35px; color: rgba(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="LC386" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="python"><span class="s" style="color: #d14;">        Args:</span></span>

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<pre style="margin: 0;"> <span id="LC388" class="line" lang="python"><span class="s" style="color: #d14;">            min_len: Minimum contaminant length.</span></span>

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="python"><span class="s" style="color: #d14;">            min_complexity: Minimum sequence complexity.</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -386,64 +392,64 @@ class Detector(SingleEndPipelineMixin, Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC392" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC393" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">min_len</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC394" class="line" lang="python">            <span class="n" style="color: #333;">min_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span></span>

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<pre style="margin: 0;">-<span id="LC389" class="line" lang="python"><span class="idiff left right">        </span></span>

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

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<pre style="margin: 0;"> <span id="LC396" class="line" lang="python">        <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_get_contaminants</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC391" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC397" class="line" lang="python"></span>

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

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<pre style="margin: 0;"> <span id="LC399" class="line" lang="python">            <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">estimate_abundance</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_sequences</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC394" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">-<span id="LC395" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_filter</span><span class="p">(</span><span class="n" style="color: #333;">match</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC396" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_report_freq</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC400" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_filter</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC402" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_report_freq</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python">                <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python">                    <span class="s" style="color: #d14;">"Filtering {} because frequency {} < {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC399" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left">match</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_report_freq</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC405" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left">_match</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_report_freq</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC406" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC401" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">min_len</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">match</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_len</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="407" style="width: 35px; color: rgba(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="LC407" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">min_len</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_len</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python">                <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC409" class="line" lang="python">                    <span class="s" style="color: #d14;">"Filtering {} because it's too short (< {} bp)"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC404" class="line" lang="python">                        <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">min_len</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="410" style="width: 35px; color: rgba(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="LC410" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">min_len</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="411" style="width: 35px; color: rgba(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="LC411" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'too short'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="412" style="width: 35px; color: rgba(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="LC412" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="413" 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="LC407" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">min_complexity</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq_complexity</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_complexity</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="408" style="width: 35px; color: rgba(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="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC413" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">min_complexity</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq_complexity</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_complexity</span><span class="p">:</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python">                <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python">                    <span class="s" style="color: #d14;">"Filtering {} because its complexity {} < {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC410" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left">match</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq_complexity</span><span class="p">,</span> <span class="n" style="color: #333;">min_complexity</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC416" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left">_match</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq_complexity</span><span class="p">,</span> <span class="n" style="color: #333;">min_complexity</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">-<span id="LC412" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">include</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'known'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_known</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC418" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">include</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'known'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_known</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python">                <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python">                    <span class="s" style="color: #d14;">"Filtering {} because it's not known"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="python">                        <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC421" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC422" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">include</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'unknown'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_known</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC423" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">include</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'unknown'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_known</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC424" class="line" lang="python">                <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC425" class="line" lang="python">                    <span class="s" style="color: #d14;">"Filtering {} because it's known"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC420" class="line" lang="python">                        <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC426" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="python">                    <span class="n" style="color: #333;">min_match_frac</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_known</span> <span class="ow" style="font-weight: 600;">and</span></span>

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<pre style="margin: 0;">-<span id="LC424" class="line" lang="python">                    <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_frac</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_match_frac</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC429" class="line" lang="python">                    <span class="n" style="color: #333;">min_match_frac</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_known</span> <span class="ow" style="font-weight: 600;">and</span></span>

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<pre style="margin: 0;">+<span id="LC430" class="line" lang="python">                    <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_frac</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">min_match_frac</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python">                <span class="n" style="color: #333;">logging</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">debug</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python">                    <span class="s" style="color: #d14;">"Filtering {} because its match_frac {} < {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left">match</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_frac</span><span class="p">,</span> <span class="n" style="color: #333;">min_match_frac</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC433" class="line" lang="python">                        <span class="n" style="color: #333;"><span class="idiff left">_match</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_</span>match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match_frac</span><span class="p">,</span> <span class="n" style="color: #333;">min_match_frac</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;">-<span id="LC430" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC436" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python">        <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span><span class="n" style="color: #333;">_filter</span><span class="p">,</span> <span class="n" style="color: #333;">matches</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python">        <span class="n" style="color: #333;">matches</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count</span><span class="p">),</span> <span class="n" style="color: #333;">reverse</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="LC433" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC439" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">limit</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC441" class="line" lang="python">            <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span><span class="p">[:</span><span class="n" style="color: #333;">limit</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC436" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC442" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">matches</span></span>

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<pre style="margin: 0;">-<span id="LC438" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC444" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC445" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_contaminants</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC446" class="line" lang="python">        <span class="s" style="color: #d14;">"""Implemention of contaminant matching.</span></span>

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<pre style="margin: 0;">-<span id="LC441" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">        </span></span></span>

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<pre style="margin: 0;">+<span id="LC447" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC448" class="line" lang="python"><span class="s" style="color: #d14;">        Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC449" class="line" lang="python"><span class="s" style="color: #d14;">            A list of :class:`Match`es.</span></span>

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<pre style="margin: 0;"> <span id="LC450" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC451" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">NotImplementedError</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC446" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC452" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC453" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">finish</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">summary</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">finish</span><span class="p">(</span><span class="n" style="color: #333;">summary</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC455" class="line" lang="python">        <span class="n" style="color: #333;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'detect'</span><span class="p">][</span><span class="s" style="color: #d14;">'matches'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">([</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="451" style="width: 35px; color: rgba(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="457" style="width: 35px; color: rgba(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">@@ -451,6 +457,7 @@ class Detector(SingleEndPipelineMixin, Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC457" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python">        <span class="p">],)</span></span>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC460" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">PairedDetector</span><span class="p">(</span><span class="n" style="color: #333;">PairedEndPipelineMixin</span><span class="p">,</span> <span class="n" style="color: #333;">Pipeline</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC462" class="line" lang="python">    <span class="s" style="color: #d14;">"""Detector for paired-end reads.</span></span>

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<pre style="margin: 0;"> <span id="LC463" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="459" style="width: 35px; color: rgba(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="466" style="width: 35px; color: rgba(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">@@ -459,7 +466,7 @@ class PairedDetector(PairedEndPipelineMixin, Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read1_detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">detector_class</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read2_detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">detector_class</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="468" style="width: 35px; color: rgba(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="LC468" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_length_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<td class="diff-line-num new_line old" data-linenumber="469" 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="LC462" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC469" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="470" style="width: 35px; color: rgba(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="LC470" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">handle_records</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">context</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">context</span><span class="p">[</span><span class="s" style="color: #d14;">'size'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="476" style="width: 35px; color: rgba(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">@@ -469,11 +476,11 @@ class PairedDetector(PairedEndPipelineMixin, Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC476" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read2_detector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_read_length</span><span class="p">(</span><span class="n" style="color: #333;">read2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC477" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_length_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handle_records</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="p">,</span> <span class="n" style="color: #333;">records</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC479" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC480" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">handle_reads</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">context</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="481" style="width: 35px; color: rgba(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="LC481" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read1_detector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handle_reads</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="p">,</span> <span class="n" style="color: #333;">read1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="482" style="width: 35px; color: rgba(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="LC482" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read2_detector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">handle_reads</span><span class="p">(</span><span class="n" style="color: #333;">context</span><span class="p">,</span> <span class="n" style="color: #333;">read2</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC476" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC483" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">finish</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">summary</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="485" style="width: 35px; color: rgba(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="LC485" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">finish</span><span class="p">(</span><span class="n" style="color: #333;">summary</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="486" style="width: 35px; color: rgba(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="LC486" class="line" lang="python">        <span class="n" style="color: #333;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'detect'</span><span class="p">][</span><span class="s" style="color: #d14;">'matches'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">([</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="484" style="width: 35px; color: rgba(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="491" style="width: 35px; color: rgba(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">@@ -484,12 +491,13 @@ class PairedDetector(PairedEndPipelineMixin, Pipeline):</td>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read2_detector</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">matches</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="492" style="width: 35px; color: rgba(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="LC492" class="line" lang="python">        <span class="p">])</span></span>

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493

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC494" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">KnownContaminantDetector</span><span class="p">(</span><span class="n" style="color: #333;">Detector</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="python">    <span class="s" style="color: #d14;">"""Test known contaminants against reads. This has linear complexity and is</span></span>

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="python"><span class="s" style="color: #d14;">    more specific than the khmer matcher, but less specific than the heuristic</span></span>

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python"><span class="s" style="color: #d14;">    matcher. It's also less sensitive since it does not try to detect unknown</span></span>

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python"><span class="s" style="color: #d14;">    contaminants.</span></span>

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<pre style="margin: 0;">-<span id="LC492" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC500" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python"><span class="s" style="color: #d14;">        known_contaminants: List of :class:`ContaminantMatcher`s.</span></span>

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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"><span class="s" style="color: #d14;">        min_kmer_match_frac: Minimum fraction of matching kmers required.</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -500,23 +508,23 @@ class KnownContaminantDetector(Detector):</td>

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="n" style="color: #333;">known_contaminants</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">known_contaminants</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_kmer_match_frac</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_kmer_match_frac</span></span>

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_min_k</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">known_contaminants</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequences</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC503" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC511" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

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<pre style="margin: 0;"> <span id="LC513" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">min_report_freq</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC514" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.1</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="515" 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="LC507" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC515" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="508" style="width: 35px; color: rgba(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="516" style="width: 35px; color: rgba(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="LC516" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_filter_seq</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="509" style="width: 35px; color: rgba(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="517" style="width: 35px; color: rgba(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="LC517" class="line" lang="python">        <span class="n" style="color: #333;">seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">super</span><span class="p">()</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_filter_seq</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="510" style="width: 35px; color: rgba(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="LC518" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">and</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">>=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_min_k</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">seq</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="512" style="width: 35px; color: rgba(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="LC520" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC513" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC521" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="522" style="width: 35px; color: rgba(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="LC522" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_contaminants</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 old_line" data-linenumber="515" style="width: 35px; color: rgba(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="LC523" class="line" lang="python">        <span class="n" style="color: #333;">contaminant_matchers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">create_contaminant_matchers</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="516" style="width: 35px; color: rgba(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="524" style="width: 35px; color: rgba(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="LC524" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">known_contaminants</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="525" style="width: 35px; color: rgba(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="LC525" class="line" lang="python">        <span class="n" style="color: #333;">counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="526" style="width: 35px; color: rgba(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="LC526" class="line" lang="python">        <span class="n" style="color: #333;">max_match_fracs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="527" 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="LC519" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="520" style="width: 35px; color: rgba(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="527" style="width: 35px; color: rgba(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="LC527" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="520" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC528" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_sequences</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="521" style="width: 35px; color: rgba(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="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">

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<pre style="margin: 0;"> <span id="LC529" class="line" lang="python">            <span class="n" style="color: #333;">seqrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reverse_complement</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC530" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contam</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contaminant_matchers</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="525" style="width: 35px; color: rgba(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">@@ -525,14 +533,14 @@ class KnownContaminantDetector(Detector):</td>

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python">                    <span class="n" style="color: #333;">counts</span><span class="p">[</span><span class="n" style="color: #333;">contam</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">max_match_fracs</span><span class="p">[</span><span class="n" style="color: #333;">contam</span><span class="p">]:</span></span>

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python">                        <span class="n" style="color: #333;">max_match_fracs</span><span class="p">[</span><span class="n" style="color: #333;">contam</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span></span>

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528

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<pre style="margin: 0;">-<span id="LC528" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC536" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python">        <span class="n" style="color: #333;">min_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ceil</span><span class="p">(</span></span>

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530

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<td class="diff-line-num new_line" data-linenumber="538" style="width: 35px; color: rgba(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="LC538" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_reads</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_min_k</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span></span>

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531

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<td class="diff-line-num new_line" data-linenumber="539" style="width: 35px; color: rgba(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="LC539" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overrep_cutoff</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">**</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_min_k</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC532" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC540" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span></span>

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python">            <span class="n" style="color: #333;">Match</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC535" class="line" lang="python">                <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">match_frac</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_match_fracs</span><span class="p">[</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]],</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC543" class="line" lang="python">                <span class="n" style="color: #333;">c</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">match_frac</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_match_fracs</span><span class="p">[</span><span class="n" style="color: #333;">c</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_line" data-linenumber="544" style="width: 35px; color: rgba(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="LC544" class="line" lang="python">                <span class="n" style="color: #333;">abundance</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])</span> <span class="o" style="font-weight: 600;">/</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_reads</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">c</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">filter</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="python">                <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_count</span><span class="p">,</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -540,44 +548,45 @@ class KnownContaminantDetector(Detector):</td>

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<pre style="margin: 0;"> <span id="LC548" class="line" lang="python">            <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC549" class="line" lang="python">        <span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC551" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">HeuristicDetector</span><span class="p">(</span><span class="n" style="color: #333;">Detector</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python">    <span class="s" style="color: #d14;">"""Use a heuristic iterative algorithm to arrive at likely contaminants.</span></span>

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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python"><span class="s" style="color: #d14;">    This is the most accurate algorithm overall, but it has quadratic complexity</span></span>

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python"><span class="s" style="color: #d14;">    and becomes too slow/memory-intenstive when n_reads > 50k.</span></span>

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC549" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">min_frequency</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.001</span><span class="p">,</span> <span class="n" style="color: #333;">min_contaminant_match_frac</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.9</span><span class="p">,</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC558" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">min_frequency</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.001</span><span class="p">,</span> <span class="n" style="color: #333;">min_contaminant_match_frac</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.9</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python">            <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="560" style="width: 35px; color: rgba(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="LC560" class="line" lang="python">        <span class="nb" style="color: #0086b3;">super</span><span class="p">(</span><span class="n" style="color: #333;">HeuristicDetector</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">__init__</span><span class="p">(</span><span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC561" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_frequency</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_frequency</span></span>

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<pre style="margin: 0;"> <span id="LC562" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_contaminant_match_frac</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">min_contaminant_match_frac</span></span>

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<pre style="margin: 0;">-<span id="LC554" class="line" lang="python"><span class="idiff left right">    </span></span>

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563

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<pre style="margin: 0;">+<span id="LC563" class="line" lang="python"></span>

</pre>

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555

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564

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="556" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

556

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<td class="diff-line-num new_line" data-linenumber="565" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

565

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">min_report_freq</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 old_line" data-linenumber="557" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

557

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<td class="diff-line-num new_line" data-linenumber="566" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

566

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.1</span> <span class="o" style="font-weight: 600;">*</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_reads</span></span>

</pre>

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558

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<td class="diff-line-num new_line old" data-linenumber="567" 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="LC558" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="559" style="width: 35px; color: rgba(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="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

567

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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="LC567" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="559" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

559

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<td class="diff-line-num new_line" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

568

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<pre style="margin: 0;"> <span id="LC568" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_contaminants</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>

</pre>

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560

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<td class="diff-line-num new_line old" data-linenumber="569" 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="LC560" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_min_count</span><span class="p">(</span><span class="n" style="color: #333;">kmer_size</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="561" style="width: 35px; color: rgba(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="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

569

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<pre style="margin: 0;">+<span id="LC569" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_min_count</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>kmer_size</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="561" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

561

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<td class="diff-line-num new_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

570

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">n_reads</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="562" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

562

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<td class="diff-line-num new_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

571

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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_frequency</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="563" 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">

563

</td>

<td class="diff-line-num new_line old" data-linenumber="572" 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="LC563" class="line" lang="python">                <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overrep_cutoff</span> <span class="o" style="font-weight: 600;">/</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="564" 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">

564

</td>

<td class="diff-line-num new_line old" data-linenumber="572" 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="LC564" class="line" lang="python">                <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;"><span class="idiff left right">**</span></span><span class="n" style="color: #333;">kmer_size</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="565" 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">

565

</td>

<td class="diff-line-num new_line old" data-linenumber="572" 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="LC565" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="566" style="width: 35px; color: rgba(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="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

572

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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="LC572" class="line" lang="python">                <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_length</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>kmer_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overrep_cutoff</span> <span class="o" style="font-weight: 600;">/</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="566" style="width: 35px; color: rgba(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="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

573

</td>

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

<pre style="margin: 0;">+<span id="LC573" class="line" lang="python">                <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="idiff left"> </span><span class="o" style="font-weight: 600;"><span class="idiff">**</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_</span>kmer_size</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="566" style="width: 35px; color: rgba(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="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

574

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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="LC574" class="line" lang="python"></span>

</pre>

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566

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<td class="diff-line-num new_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

575

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="python">        <span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="567" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

567

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<td class="diff-line-num new_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

576

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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python">        <span class="n" style="color: #333;">kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="568" 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">

568

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<td class="diff-line-num new_line old" data-linenumber="577" 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="LC568" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="569" style="width: 35px; color: rgba(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="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

577

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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="LC577" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="569" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

569

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<td class="diff-line-num new_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

578

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<pre style="margin: 0;"> <span id="LC578" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_sequences</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="570" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

570

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<td class="diff-line-num new_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

579

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<pre style="margin: 0;"> <span id="LC579" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="571" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

571

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<td class="diff-line-num new_line" data-linenumber="580" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

580

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<pre style="margin: 0;"> <span id="LC580" class="line" lang="python">                <span class="n" style="color: #333;">kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmer_size</span><span class="p">)]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="572" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

572

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<td class="diff-line-num new_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python">                <span class="n" style="color: #333;">kmers</span><span class="p">[</span><span class="n" style="color: #333;">kmer</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="573" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

573

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<td class="diff-line-num new_line" data-linenumber="582" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

582

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

<pre style="margin: 0;"> <span id="LC582" class="line" lang="python">                <span class="n" style="color: #333;">kmers</span><span class="p">[</span><span class="n" style="color: #333;">kmer</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="574" 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">

574

</td>

<td class="diff-line-num new_line old" data-linenumber="583" 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="LC574" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="575" style="width: 35px; color: rgba(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="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

583

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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="LC583" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="575" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

575

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<td class="diff-line-num new_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

584

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

<pre style="margin: 0;"> <span id="LC584" class="line" lang="python">        <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="576" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

576

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<td class="diff-line-num new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

585

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

<pre style="margin: 0;"> <span id="LC585" class="line" lang="python">        <span class="n" style="color: #333;">cur</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="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

577

</td>

<td class="diff-line-num new_line" data-linenumber="586" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

586

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<pre style="margin: 0;"> <span id="LC586" class="line" lang="python">        <span class="n" style="color: #333;">results</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="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

578

</td>

<td class="diff-line-num new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

587

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

<pre style="margin: 0;"> <span id="LC587" class="line" lang="python">        <span class="n" style="color: #333;">result_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">set</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

579

</td>

<td class="diff-line-num new_line" data-linenumber="588" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

588

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

<pre style="margin: 0;"> <span id="LC588" class="line" lang="python">        <span class="n" style="color: #333;">min_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_min_count</span><span class="p">(</span><span class="n" style="color: #333;">kmer_size</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="580" 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">

580

</td>

<td class="diff-line-num new_line old" data-linenumber="589" 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="LC580" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="581" style="width: 35px; color: rgba(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="589" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

589

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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="LC589" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="581" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

581

</td>

<td class="diff-line-num new_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

590

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

<pre style="margin: 0;"> <span id="LC590" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Identify candidate kmers for increasing values of k</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC591" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="bp" style="color: #999;">True</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC592" class="line" lang="python">            <span class="n" style="color: #333;">all_seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="585" style="width: 35px; color: rgba(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="594" style="width: 35px; color: rgba(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">@@ -585,10 +594,10 @@ class HeuristicDetector(Detector):</td>

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<td class="diff-line-num old_line" data-linenumber="585" style="width: 35px; color: rgba(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="594" style="width: 35px; color: rgba(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="LC594" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">min_count</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="586" style="width: 35px; color: rgba(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="595" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

595

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<pre style="margin: 0;"> <span id="LC595" class="line" lang="python">                    <span class="n" style="color: #333;">cur</span><span class="p">[</span><span class="n" style="color: #333;">kmer</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">)</span></span>

</pre>

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587

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<td class="diff-line-num new_line" data-linenumber="596" style="width: 35px; color: rgba(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="LC596" class="line" lang="python">                    <span class="n" style="color: #333;">all_seqs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="597" 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="LC588" class="line" lang="python"><span class="idiff left right">            </span></span>

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<td class="diff-line-num new old_line" data-linenumber="589" style="width: 35px; color: rgba(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="LC597" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="589" style="width: 35px; color: rgba(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="598" style="width: 35px; color: rgba(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="LC598" 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;">all_seqs</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="590" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

590

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<td class="diff-line-num new_line" data-linenumber="599" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

599

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<pre style="margin: 0;"> <span id="LC599" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

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<td class="diff-line-num old old_line" data-linenumber="591" 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">

591

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<pre style="margin: 0;">-<span id="LC591" class="line" lang="python"><span class="idiff left right">            </span></span>

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<td class="diff-line-num new old_line" data-linenumber="592" style="width: 35px; color: rgba(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="600" style="width: 35px; color: rgba(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="LC600" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="592" style="width: 35px; color: rgba(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="601" style="width: 35px; color: rgba(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="LC601" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prev</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="593" style="width: 35px; color: rgba(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="602" style="width: 35px; color: rgba(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="LC602" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">kmer</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="n" style="color: #333;">seqs</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">prev</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="594" style="width: 35px; color: rgba(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="603" style="width: 35px; color: rgba(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="LC603" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="596" style="width: 35px; color: rgba(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="605" style="width: 35px; color: rgba(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">@@ -596,7 +605,7 @@ class HeuristicDetector(Detector):</td>

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<td class="diff-line-num old_line" data-linenumber="596" style="width: 35px; color: rgba(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="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

605

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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python">                            <span class="n" style="color: #333;">sequence_complexity</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mf" style="color: #099;">1.0</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="597" style="width: 35px; color: rgba(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="606" style="width: 35px; color: rgba(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="LC606" class="line" lang="python">                        <span class="n" style="color: #333;">results</span><span class="p">[</span><span class="n" style="color: #333;">kmer</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</span></span>

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<td class="diff-line-num new_line" data-linenumber="607" style="width: 35px; color: rgba(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="LC607" class="line" lang="python">                        <span class="n" style="color: #333;">result_seqs</span><span class="p">[</span><span class="n" style="color: #333;">kmer</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC599" class="line" lang="python"><span class="idiff left right">            </span></span>

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<pre style="margin: 0;">+<span id="LC608" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python">            <span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="601" style="width: 35px; color: rgba(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="610" style="width: 35px; color: rgba(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="LC610" class="line" lang="python">            <span class="n" style="color: #333;">kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()])</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="611" style="width: 35px; color: rgba(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="LC611" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">all_seqs</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="604" style="width: 35px; color: rgba(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="613" style="width: 35px; color: rgba(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">@@ -604,17 +613,16 @@ class HeuristicDetector(Detector):</td>

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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python">                    <span class="n" style="color: #333;">kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seq</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">:(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">kmer_size</span><span class="p">)]</span></span>

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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python">                    <span class="n" style="color: #333;">kmers</span><span class="p">[</span><span class="n" style="color: #333;">kmer</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python">                    <span class="n" style="color: #333;">kmers</span><span class="p">[</span><span class="n" style="color: #333;">kmer</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="616" 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="LC607" class="line" lang="python"><span class="idiff left right">            </span></span>

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<pre style="margin: 0;">+<span id="LC616" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="608" style="width: 35px; color: rgba(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="617" style="width: 35px; color: rgba(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="LC617" class="line" lang="python">            <span class="n" style="color: #333;">min_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_min_count</span><span class="p">(</span><span class="n" style="color: #333;">kmer_size</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="609" style="width: 35px; color: rgba(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="618" style="width: 35px; color: rgba(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="LC618" class="line" lang="python">            <span class="n" style="color: #333;">prev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cur</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="610" style="width: 35px; color: rgba(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="619" style="width: 35px; color: rgba(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="LC619" class="line" lang="python">            <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC611" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC620" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python">        <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">())</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC613" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC622" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Now merge overlapping sequences by length and frequency to eliminate</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="615" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

615

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<td class="diff-line-num new_line" data-linenumber="624" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

624

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<pre style="margin: 0;"> <span id="LC624" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># redundancy in the set of candidate kmers.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="616" 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="625" 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="LC616" class="line" lang="python">        <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">i</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="617" 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">

617

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<td class="diff-line-num new_line old" data-linenumber="625" 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="LC617" class="line" lang="python">        <span class="n" style="color: #333;">cur</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">results</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 old_line" data-linenumber="618" style="width: 35px; color: rgba(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="625" style="width: 35px; color: rgba(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="LC625" class="line" lang="python">        <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">r</span><span class="p">:</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">log</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="n" style="color: #333;">reverse</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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618

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<td class="diff-line-num new_line" data-linenumber="626" style="width: 35px; color: rgba(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="LC626" class="line" lang="python">        <span class="n" style="color: #333;">merged</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="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

619

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<td class="diff-line-num new_line" data-linenumber="627" style="width: 35px; color: rgba(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="LC627" class="line" lang="python">        <span class="n" style="color: #333;">unmerged</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="620" style="width: 35px; color: rgba(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="628" style="width: 35px; color: rgba(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="LC628" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">1</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="634" style="width: 35px; color: rgba(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="642" style="width: 35px; color: rgba(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">@@ -634,76 +642,81 @@ class HeuristicDetector(Detector):</td>

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<td class="diff-line-num new_line" data-linenumber="642" style="width: 35px; color: rgba(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="LC642" class="line" lang="python">            <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">unmerged</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="635" style="width: 35px; color: rgba(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="643" style="width: 35px; color: rgba(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="LC643" class="line" lang="python">            <span class="n" style="color: #333;">unmerged</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_line" data-linenumber="644" style="width: 35px; color: rgba(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="LC644" class="line" lang="python">        <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">merged</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">results</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="645" 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="LC637" class="line" lang="python"><span class="idiff left right">        </span></span>

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<td class="diff-line-num new old_line" data-linenumber="638" style="width: 35px; color: rgba(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="645" style="width: 35px; color: rgba(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="LC645" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="638" style="width: 35px; color: rgba(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="646" style="width: 35px; color: rgba(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="LC646" 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;">results</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="639" style="width: 35px; color: rgba(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="647" style="width: 35px; color: rgba(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="LC647" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="p">[]</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="648" 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="LC640" class="line" lang="python"><span class="idiff left right">        </span></span>

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<td class="diff-line-num new new_line" data-linenumber="648" style="width: 35px; color: rgba(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="LC648" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC649" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO: For each retained match, pull out the longest sequence that</span></span>

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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># matches to have a better shot of identifying long adapters that</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># appear in full very infrequently</span></span>

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<pre style="margin: 0;">-<span id="LC644" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC652" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC653" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Re-sort by frequency</span></span>

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<pre style="margin: 0;">-<span id="LC646" class="line" lang="python">        <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;"><span class="idiff left">i</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">i</span></span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">reverse</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="LC654" class="line" lang="python">        <span class="n" style="color: #333;">results</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;">=</span><span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;"><span class="idiff left">r</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">r</span></span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">reverse</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="LC655" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Keep anything that's within 50% of the top hit</span></span>

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># TODO: make this user-configurable?</span></span>

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="python">        <span class="n" style="color: #333;">min_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">results</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="python">        <span class="n" style="color: #333;">results</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_count</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC659" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Convert to matches</span></span>

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<pre style="margin: 0;"> <span id="LC660" class="line" lang="python">        <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<pre style="margin: 0;">-<span id="LC653" class="line" lang="python">            <span class="n" style="color: #333;">Match</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">result_seqs</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]])</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC661" class="line" lang="python">            <span class="n" style="color: #333;">Match</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">],</span> <span class="n" style="color: #333;">reads</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">result_seqs</span><span class="p">[</span><span class="n" style="color: #333;">x</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]])</span></span>

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">results</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC655" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC664" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">known_contaminants</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Match to known sequences</span></span>

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<td class="diff-line-num old_line" data-linenumber="658" style="width: 35px; color: rgba(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="LC666" class="line" lang="python">            <span class="n" style="color: #333;">contaminants</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">create_contaminant_matchers</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">known_contaminants</span><span class="p">,</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC668" class="line" lang="python">            <span class="n" style="color: #333;">known</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python">            <span class="n" style="color: #333;">unknown</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC662" class="line" lang="python"><span class="idiff left right">            </span></span>

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<pre style="margin: 0;">-<span id="LC663" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find_best_match</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">best_matches</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">best_match_frac</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC670" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC671" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">find_best_match</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">_seq</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_best_matches</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">_</span>best_match_frac</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC672" class="line" lang="python">                <span class="s" style="color: #d14;">"""Find best contaminant matches to `seq`.</span></span>

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<pre style="margin: 0;"> <span id="LC673" class="line" lang="python"><span class="s" style="color: #d14;">                """</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC666" class="line" lang="python">                <span class="n" style="color: #333;">seqrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reverse_complement</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="674" 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="LC667" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contam</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contaminants</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC668" class="line" lang="python">                    <span class="n" style="color: #333;">match_frac1</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="p">,</span> <span class="n" style="color: #333;">compare_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">contam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC669" class="line" lang="python">                        <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqrc</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC670" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match_frac1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">best_match_frac</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC674" class="line" lang="python">                <span class="n" style="color: #333;">seqrc</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">reverse_complement</span><span class="p">(</span><span class="n" style="color: #333;">_seq</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC675" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC676" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_contam</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">contaminants</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC677" class="line" lang="python">                    <span class="n" style="color: #333;">match_frac1</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="p">,</span> <span class="n" style="color: #333;">compare_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_contam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">match</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC678" class="line" lang="python">                        <span class="n" style="color: #333;">_seq</span><span class="p">,</span> <span class="n" style="color: #333;">seqrc</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC679" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match_frac1</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">_best_match_frac</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC680" class="line" lang="python">                        <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;"> <span id="LC681" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC673" class="line" lang="python">                            <span class="n" style="color: #333;">contam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">compare_seq</span> <span class="ow" style="font-weight: 600;">or</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC682" class="line" lang="python">                            <span class="n" style="color: #333;"><span class="idiff left right">_</span>contam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">compare_seq</span> <span class="ow" style="font-weight: 600;">or</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC683" class="line" lang="python">                            <span class="n" style="color: #333;">align</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC675" class="line" lang="python">                                <span class="n" style="color: #333;">compare_seq</span><span class="p">,</span> <span class="n" style="color: #333;">contam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC684" class="line" lang="python">                                <span class="n" style="color: #333;">compare_seq</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>contam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC685" class="line" lang="python">                                <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_contaminant_match_frac</span><span class="p">)):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC677" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">match_frac1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">best_match_frac</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC678" class="line" lang="python">                                <span class="n" style="color: #333;">match_frac1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">best_match_frac</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span></span>

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<pre style="margin: 0;">-<span id="LC679" class="line" lang="python">                                <span class="n" style="color: #333;">match_frac2</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">best_match_frac</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">])):</span></span>

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680

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<pre style="margin: 0;">-<span id="LC680" class="line" lang="python">                            <span class="n" style="color: #333;">best_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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681

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<pre style="margin: 0;">-<span id="LC681" class="line" lang="python">                            <span class="n" style="color: #333;">best_match_frac</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">match_frac1</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="p">)</span></span>

</pre>

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682

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<pre style="margin: 0;">-<span id="LC682" class="line" lang="python">                        <span class="n" style="color: #333;">best_matches</span><span class="p">[</span><span class="n" style="color: #333;">contam</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

</pre>

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686

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<pre style="margin: 0;">+<span id="LC686" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span></span>

</pre>

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687

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<pre style="margin: 0;">+<span id="LC687" class="line" lang="python">                            <span class="n" style="color: #333;">match_frac1</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_best_match_frac</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span></span>

</pre>

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688

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<pre style="margin: 0;">+<span id="LC688" class="line" lang="python">                                <span class="n" style="color: #333;">match_frac1</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">_best_match_frac</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">and</span></span>

</pre>

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689

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="python">                                <span class="n" style="color: #333;">match_frac2</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">_best_match_frac</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="python">                            <span class="p">)</span></span>

</pre>

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691

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="python">                        <span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC692" class="line" lang="python">                            <span class="n" style="color: #333;">_best_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC693" class="line" lang="python">                            <span class="n" style="color: #333;">_best_match_frac</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">match_frac1</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC694" class="line" lang="python">                        <span class="n" style="color: #333;">_best_matches</span><span class="p">[</span><span class="n" style="color: #333;">_contam</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC695" class="line" lang="python">                            <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">match_frac1</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac2</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC684" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">best_matches</span><span class="p">,</span> <span class="n" style="color: #333;">best_match_frac</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC685" class="line" lang="python">            </span>

</pre>

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<pre style="margin: 0;">+<span id="LC696" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC697" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">_best_matches</span><span class="p">,</span> <span class="n" style="color: #333;">_best_match_frac</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC698" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="699" style="width: 35px; color: rgba(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="LC699" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">matches</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="687" style="width: 35px; color: rgba(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="700" style="width: 35px; color: rgba(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="LC700" class="line" lang="python">                <span class="n" style="color: #333;">best_matches</span><span class="p">,</span> <span class="n" style="color: #333;">best_match_frac</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_best_match</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="688" style="width: 35px; color: rgba(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="701" style="width: 35px; color: rgba(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="LC701" class="line" lang="python">                    <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="p">{},</span> <span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">min_contaminant_match_frac</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_line old" data-linenumber="702" 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="LC689" class="line" lang="python"><span class="idiff left right">                </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="690" style="width: 35px; color: rgba(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="LC702" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="690" style="width: 35px; color: rgba(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="703" style="width: 35px; color: rgba(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="LC703" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longest_match</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="691" style="width: 35px; color: rgba(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="704" style="width: 35px; color: rgba(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="LC704" class="line" lang="python">                    <span class="n" style="color: #333;">best_matches</span><span class="p">,</span> <span class="n" style="color: #333;">best_match_frac</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_best_match</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="692" style="width: 35px; color: rgba(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="705" style="width: 35px; color: rgba(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="LC705" class="line" lang="python">                        <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">longest_match</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">best_matches</span><span class="p">,</span> <span class="n" style="color: #333;">best_match_frac</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="693" 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="706" 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="LC693" class="line" lang="python"><span class="idiff left right">                </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="694" style="width: 35px; color: rgba(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="LC706" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="694" style="width: 35px; color: rgba(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="707" style="width: 35px; color: rgba(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="LC707" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">best_matches</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="695" 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">

695

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<td class="diff-line-num new_line old" data-linenumber="708" 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="LC695" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contam</span><span class="p">,</span> <span class="n" style="color: #333;">match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">best_matches</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="696" 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="708" 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="LC696" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">contam</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">known</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">match</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">known</span><span class="p">[</span><span class="n" style="color: #333;">contam</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="697" 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="708" 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="LC697" class="line" lang="python">                            <span class="n" style="color: #333;">known</span><span class="p">[</span><span class="n" style="color: #333;">contam</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

708

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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="LC708" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contam</span><span class="p">,</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">best_matches</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

709

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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="LC709" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">contam</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">known</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">known</span><span class="p">[</span><span class="n" style="color: #333;">contam</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="698" style="width: 35px; color: rgba(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="710" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

710

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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="LC710" class="line" lang="python">                            <span class="n" style="color: #333;">known</span><span class="p">[</span><span class="n" style="color: #333;">contam</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">_</span>match</span></span>

</pre>

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698

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<td class="diff-line-num new_line" data-linenumber="711" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

711

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<pre style="margin: 0;"> <span id="LC711" 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 old_line" data-linenumber="699" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

699

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<td class="diff-line-num new_line" data-linenumber="712" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

712

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python">                    <span class="n" style="color: #333;">unknown</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">match</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="700" 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">

700

</td>

<td class="diff-line-num new_line old" data-linenumber="713" 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="LC700" class="line" lang="python"><span class="idiff left right">            </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="701" style="width: 35px; color: rgba(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="713" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

713

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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="LC713" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="701" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

701

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<td class="diff-line-num new_line" data-linenumber="714" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

714

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<pre style="margin: 0;"> <span id="LC714" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># resolve many-many relationships</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="702" 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">

702

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<td class="diff-line-num new_line old" data-linenumber="715" 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="LC702" class="line" lang="python"><span class="idiff left right">            </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="703" style="width: 35px; color: rgba(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="715" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

715

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<pre style="margin: 0;">+<span id="LC715" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="703" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

703

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<td class="diff-line-num new_line" data-linenumber="716" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

716

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python">            <span class="n" style="color: #333;">new_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="k" style="font-weight: 600;">lambda</span><span class="p">:</span> <span class="p">[])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="704" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

704

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<td class="diff-line-num new_line" data-linenumber="717" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

717

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<pre style="margin: 0;"> <span id="LC717" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contam</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">known</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="705" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

705

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<td class="diff-line-num new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

718

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<pre style="margin: 0;"> <span id="LC718" class="line" lang="python">                <span class="n" style="color: #333;">new_matches</span><span class="p">[</span><span class="n" style="color: #333;">match</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="n" style="color: #333;">contam</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="706" 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">

706

</td>

<td class="diff-line-num new_line old" data-linenumber="719" 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="LC706" class="line" lang="python"><span class="idiff left right">            </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="707" style="width: 35px; color: rgba(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="719" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

719

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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="LC719" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="707" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

707

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<td class="diff-line-num new_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python">            <span class="n" style="color: #333;">known</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="708" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

708

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<td class="diff-line-num new_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

721

</td>

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

<pre style="margin: 0;"> <span id="LC721" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">match</span><span class="p">,</span> <span class="n" style="color: #333;">contams</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">new_matches</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="709" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

709

</td>

<td class="diff-line-num new_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

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

<pre style="margin: 0;"> <span id="LC722" 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;">contams</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">1</span><span class="p">:</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="720" style="width: 35px; color: rgba(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="733" style="width: 35px; color: rgba(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">@@ -720,17 +733,18 @@ class HeuristicDetector(Detector):</td>

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<td class="diff-line-num old_line" data-linenumber="720" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

720

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<td class="diff-line-num new_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

733

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<pre style="margin: 0;"> <span id="LC733" class="line" lang="python">                        <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_contaminant</span><span class="p">(</span><span class="n" style="color: #333;">contam</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">match_frac</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

721

</td>

<td class="diff-line-num new_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

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

<pre style="margin: 0;"> <span id="LC734" 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 old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

722

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<td class="diff-line-num new_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

735

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

<pre style="margin: 0;"> <span id="LC735" class="line" lang="python">                        <span class="n" style="color: #333;">names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">contam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">names</span><span class="p">)</span></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="723" 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">

723

</td>

<td class="diff-line-num new_line old" data-linenumber="736" 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="LC723" class="line" lang="python">                        <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">set</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">contam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff right">,))</span></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="724" style="width: 35px; color: rgba(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="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

736

</td>

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

<pre style="margin: 0;">+<span id="LC736" class="line" lang="python">                        <span class="n" style="color: #333;">seqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">{(</span></span><span class="n" style="color: #333;"><span class="idiff">contam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff right">,)}</span></span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

724

</td>

<td class="diff-line-num new_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

737

</td>

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

<pre style="margin: 0;"> <span id="LC737" class="line" lang="python">                        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">other_contam</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">equiv</span><span class="p">:</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="725" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

725

</td>

<td class="diff-line-num new_line" data-linenumber="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

738

</td>

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

<pre style="margin: 0;"> <span id="LC738" class="line" lang="python">                            <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">update</span><span class="p">(</span><span class="n" style="color: #333;">other_contam</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">names</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="726" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

726

</td>

<td class="diff-line-num new_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

</td>

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

<pre style="margin: 0;"> <span id="LC739" class="line" lang="python">                            <span class="n" style="color: #333;">seqs</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">other_contam</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="727" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

727

</td>

<td class="diff-line-num new_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

</td>

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

<pre style="margin: 0;"> <span id="LC740" class="line" lang="python">                        <span class="n" style="color: #333;">match</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_known</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">seqs</span><span class="p">),</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">match_frac</span><span class="p">)</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="728" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

728

</td>

<td class="diff-line-num new_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

</td>

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

<pre style="margin: 0;"> <span id="LC741" class="line" lang="python">                <span class="n" style="color: #333;">known</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">match</span><span class="p">)</span></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="729" 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">

729

</td>

<td class="diff-line-num new_line old" data-linenumber="742" 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="LC729" class="line" lang="python"><span class="idiff left right">            </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="730" style="width: 35px; color: rgba(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="742" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

742

</td>

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

<pre style="margin: 0;">+<span id="LC742" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="730" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

730

</td>

<td class="diff-line-num new_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

</td>

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

<pre style="margin: 0;"> <span id="LC743" class="line" lang="python">            <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">known</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">unknown</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="731" 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">

731

</td>

<td class="diff-line-num new_line old" data-linenumber="744" 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="LC731" class="line" lang="python"><span class="idiff left right">        </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="732" style="width: 35px; color: rgba(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="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

744

</td>

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

<pre style="margin: 0;">+<span id="LC744" class="line" lang="python"></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="732" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

732

</td>

<td class="diff-line-num new_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

</td>

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

<pre style="margin: 0;"> <span id="LC745" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matches</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="733" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

733

</td>

<td class="diff-line-num new_line" data-linenumber="746" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

746

</td>

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

<pre style="margin: 0;"> <span id="LC746" 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="734" style="width: 35px; color: rgba(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="747" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

747

</td>

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

<pre style="margin: 0;">+<span id="LC747" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="734" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

734

</td>

<td class="diff-line-num new_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

</td>

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

<pre style="margin: 0;"> <span id="LC748" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">KhmerDetector</span><span class="p">(</span><span class="n" style="color: #333;">Detector</span><span class="p">):</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="735" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

735

</td>

<td class="diff-line-num new_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

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

<pre style="margin: 0;"> <span id="LC749" class="line" lang="python">    <span class="s" style="color: #d14;">"""Identify contaminants based on kmer frequency using a fast kmer counting</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="736" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

736

</td>

<td class="diff-line-num new_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

750

</td>

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

<pre style="margin: 0;"> <span id="LC750" class="line" lang="python"><span class="s" style="color: #d14;">    approach (as implemented in the khmer library). This approach is fast but</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="739" style="width: 35px; color: rgba(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="753" style="width: 35px; color: rgba(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">@@ -739,7 +753,7 @@ class KhmerDetector(Detector):</td>

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<td class="diff-line-num old_line" data-linenumber="739" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

739

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<td class="diff-line-num new_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

753

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<pre style="margin: 0;"> <span id="LC753" class="line" lang="python">    <span class="o" style="font-weight: 600;">@</span><span class="nb" style="color: #0086b3;">property</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="740" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

740

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<td class="diff-line-num new_line" data-linenumber="754" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

754

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<pre style="margin: 0;"> <span id="LC754" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">min_report_freq</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 old_line" data-linenumber="741" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

741

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<td class="diff-line-num new_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

755

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<pre style="margin: 0;"> <span id="LC755" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="mf" style="color: #099;">0.0001</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="742" 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">

742

</td>

<td class="diff-line-num new_line old" data-linenumber="756" 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="LC742" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="743" style="width: 35px; color: rgba(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="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

756

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<pre style="margin: 0;">+<span id="LC756" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="743" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

743

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<td class="diff-line-num new_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

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<pre style="margin: 0;"> <span id="LC757" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_get_contaminants</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 old_line" data-linenumber="744" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

744

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<td class="diff-line-num new_line" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

758

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<pre style="margin: 0;"> <span id="LC758" class="line" lang="python">        <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">khmer</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">Countgraph</span><span class="p">,</span> <span class="n" style="color: #333;">khmer_args</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="745" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

745

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<td class="diff-line-num new_line" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

759

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<pre style="margin: 0;"> <span id="LC759" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># assuming all sequences are same length</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="748" style="width: 35px; color: rgba(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="762" style="width: 35px; color: rgba(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">@@ -748,43 +762,43 @@ class KhmerDetector(Detector):</td>

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<td class="diff-line-num old_line" data-linenumber="748" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

748

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<td class="diff-line-num new_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

762

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<pre style="margin: 0;"> <span id="LC762" class="line" lang="python">        <span class="n" style="color: #333;">countgraph</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Countgraph</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="749" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

749

</td>

<td class="diff-line-num new_line" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

763

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<pre style="margin: 0;"> <span id="LC763" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span><span class="p">,</span> <span class="n" style="color: #333;">tablesize</span><span class="p">,</span> <span class="n" style="color: #333;">khmer_args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DEFAULT_N_TABLES</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="750" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

750

</td>

<td class="diff-line-num new_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

764

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

<pre style="margin: 0;"> <span id="LC764" class="line" lang="python">        <span class="n" style="color: #333;">countgraph</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">set_use_bigcount</span><span class="p">(</span><span class="bp" style="color: #999;">True</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="751" 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">

751

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<td class="diff-line-num new_line old" data-linenumber="765" 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="LC751" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="752" style="width: 35px; color: rgba(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="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

765

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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="LC765" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="752" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

752

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<td class="diff-line-num new_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

766

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<pre style="margin: 0;"> <span id="LC766" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_read_sequences</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="753" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

753

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<td class="diff-line-num new_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

767

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

<pre style="margin: 0;"> <span id="LC767" class="line" lang="python">            <span class="n" style="color: #333;">countgraph</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">consume_and_tag</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="754" 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">

754

</td>

<td class="diff-line-num new_line old" data-linenumber="768" 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="LC754" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="755" style="width: 35px; color: rgba(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="768" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

768

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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="LC768" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

755

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<td class="diff-line-num new_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

769

</td>

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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python">        <span class="n" style="color: #333;">n_expected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">math</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ceil</span><span class="p">(</span><span class="n" style="color: #333;">tablesize</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="mi" style="color: #099;">4</span><span class="o" style="font-weight: 600;">**</span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

756

</td>

<td class="diff-line-num new_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

770

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<pre style="margin: 0;"> <span id="LC770" class="line" lang="python">        <span class="n" style="color: #333;">min_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">n_expected</span> <span class="o" style="font-weight: 600;">*</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">overrep_cutoff</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

757

</td>

<td class="diff-line-num new_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

771

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

<pre style="margin: 0;"> <span id="LC771" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">min_count</span> <span class="o" style="font-weight: 600;">>=</span> <span class="mi" style="color: #099;">2</span><span class="o" style="font-weight: 600;">**</span><span class="mi" style="color: #099;">16</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="758" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

758

</td>

<td class="diff-line-num new_line" data-linenumber="772" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

772

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<pre style="margin: 0;"> <span id="LC772" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="759" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

759

</td>

<td class="diff-line-num new_line" data-linenumber="773" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

773

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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python">                <span class="s" style="color: #d14;">"The minimum count for an over-represented k-kmer {} is "</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="760" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

760

</td>

<td class="diff-line-num new_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

774

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

<pre style="margin: 0;"> <span id="LC774" class="line" lang="python">                <span class="s" style="color: #d14;">"greater than the max khmer count (2^16)"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">min_count</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="761" 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">

761

</td>

<td class="diff-line-num new_line old" data-linenumber="775" 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="LC761" class="line" lang="python"><span class="idiff left right">    </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="762" style="width: 35px; color: rgba(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="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

775

</td>

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

<pre style="margin: 0;">+<span id="LC775" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

762

</td>

<td class="diff-line-num new_line" data-linenumber="776" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

776

</td>

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

<pre style="margin: 0;"> <span id="LC776" class="line" lang="python">        <span class="n" style="color: #333;">candidates</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></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="763" 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">

763

</td>

<td class="diff-line-num new_line old" data-linenumber="777" 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="LC763" class="line" lang="python"><span class="idiff left right">        </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="764" style="width: 35px; color: rgba(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="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

777

</td>

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

<pre style="margin: 0;">+<span id="LC777" class="line" lang="python"></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

764

</td>

<td class="diff-line-num new_line" data-linenumber="778" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

778

</td>

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

<pre style="margin: 0;"> <span id="LC778" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tag</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">countgraph</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_tagset</span><span class="p">():</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="765" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

765

</td>

<td class="diff-line-num new_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

</td>

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

<pre style="margin: 0;"> <span id="LC779" class="line" lang="python">            <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">countgraph</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">tag</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="766" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

766

</td>

<td class="diff-line-num new_line" data-linenumber="780" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

780

</td>

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

<pre style="margin: 0;"> <span id="LC780" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">min_count</span><span class="p">:</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="767" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

767

</td>

<td class="diff-line-num new_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

781

</td>

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

<pre style="margin: 0;"> <span id="LC781" class="line" lang="python">                <span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">tag</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">count</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="768" 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">

768

</td>

<td class="diff-line-num new_line old" data-linenumber="782" 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="LC768" class="line" lang="python"><span class="idiff left right">        </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="769" style="width: 35px; color: rgba(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="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

782

</td>

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

<pre style="margin: 0;">+<span id="LC782" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="769" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

769

</td>

<td class="diff-line-num new_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

</td>

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

<pre style="margin: 0;"> <span id="LC783" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">known_contaminants</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="770" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

770

</td>

<td class="diff-line-num new_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

</td>

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

<pre style="margin: 0;"> <span id="LC784" class="line" lang="python">            <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="771" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

771

</td>

<td class="diff-line-num new_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

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<pre style="margin: 0;"> <span id="LC785" class="line" lang="python">            <span class="n" style="color: #333;">seen</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="772" 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">

772

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<td class="diff-line-num new_line old" data-linenumber="786" 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="LC772" class="line" lang="python"><span class="idiff left right">            </span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="773" 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">

773

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<td class="diff-line-num new_line old" data-linenumber="786" 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="LC773" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">match</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="774" style="width: 35px; color: rgba(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="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

786

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<pre style="margin: 0;">+<span id="LC786" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="774" style="width: 35px; color: rgba(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="787" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

787

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<pre style="margin: 0;">+<span id="LC787" class="line" lang="python">            <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">match</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>kmer</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="774" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

774

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<td class="diff-line-num new_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

788

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<pre style="margin: 0;"> <span id="LC788" class="line" lang="python">                <span class="s" style="color: #d14;">"""Returns the frequency of `kmer` in `candidates`.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="775" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

775

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<td class="diff-line-num new_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

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<pre style="margin: 0;"> <span id="LC789" class="line" lang="python"><span class="s" style="color: #d14;">                """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="776" 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">

776

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<td class="diff-line-num new_line old" data-linenumber="790" 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="LC776" class="line" lang="python">                <span class="n" style="color: #333;">freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">candidates</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;">kmer</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 old_line" data-linenumber="777" style="width: 35px; color: rgba(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="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

790

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<pre style="margin: 0;">+<span id="LC790" class="line" lang="python">                <span class="n" style="color: #333;">freq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">candidates</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>kmer</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 old_line" data-linenumber="777" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

777

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<td class="diff-line-num new_line" data-linenumber="791" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

791

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<pre style="margin: 0;"> <span id="LC791" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">freq</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="778" 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">

778

</td>

<td class="diff-line-num new_line old" data-linenumber="792" 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="LC778" class="line" lang="python">                    <span class="n" style="color: #333;">seen</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;">kmer</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="779" style="width: 35px; color: rgba(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="792" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

792

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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="LC792" class="line" lang="python">                    <span class="n" style="color: #333;">seen</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">_</span>kmer</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="779" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

779

</td>

<td class="diff-line-num new_line" data-linenumber="793" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

793

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

<pre style="margin: 0;"> <span id="LC793" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">freq</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="780" 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">

780

</td>

<td class="diff-line-num new_line old" data-linenumber="794" 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="LC780" class="line" lang="python"><span class="idiff left right">            </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="781" style="width: 35px; color: rgba(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="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

794

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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="LC794" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="781" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

781

</td>

<td class="diff-line-num new_line" data-linenumber="795" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

795

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

<pre style="margin: 0;"> <span id="LC795" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">names</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">known_contaminants</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iter_sequences</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="782" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

782

</td>

<td class="diff-line-num new_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

796

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

<pre style="margin: 0;"> <span id="LC796" class="line" lang="python">                <span class="n" style="color: #333;">seqlen</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</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="783" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

783

</td>

<td class="diff-line-num new_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

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

<pre style="margin: 0;"> <span id="LC797" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;"><</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="784" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

784

</td>

<td class="diff-line-num new_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

798

</td>

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

<pre style="margin: 0;"> <span id="LC798" class="line" lang="python">                    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot check {}; sequence is shorter than {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="785" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

785

</td>

<td class="diff-line-num new_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

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

<pre style="margin: 0;"> <span id="LC799" class="line" lang="python">                        <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">names</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="786" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

786

</td>

<td class="diff-line-num new_line" data-linenumber="800" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

800

</td>

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

<pre style="margin: 0;"> <span id="LC800" class="line" lang="python">                    <span class="k" style="font-weight: 600;">continue</span></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="787" 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">

787

</td>

<td class="diff-line-num new_line old" data-linenumber="801" 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="LC787" class="line" lang="python"><span class="idiff left right">                </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="788" style="width: 35px; color: rgba(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="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

801

</td>

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

<pre style="margin: 0;">+<span id="LC801" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="788" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

788

</td>

<td class="diff-line-num new_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

802

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<pre style="margin: 0;"> <span id="LC802" class="line" lang="python">                <span class="n" style="color: #333;">n_kmers</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">seqlen</span> <span class="o" style="font-weight: 600;">-</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">kmer_size</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="789" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

789

</td>

<td class="diff-line-num new_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

803

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

<pre style="margin: 0;"> <span id="LC803" class="line" lang="python">                <span class="n" style="color: #333;">num_matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="790" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

790

</td>

<td class="diff-line-num new_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

804

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

<pre style="margin: 0;"> <span id="LC804" class="line" lang="python">                <span class="n" style="color: #333;">match_counts</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</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="797" style="width: 35px; color: rgba(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="811" style="width: 35px; color: rgba(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">@@ -797,34 +811,36 @@ class KhmerDetector(Detector):</td>

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<td class="diff-line-num old_line" data-linenumber="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

797

</td>

<td class="diff-line-num new_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

811

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

<pre style="margin: 0;"> <span id="LC811" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">kmer_count</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="798" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

798

</td>

<td class="diff-line-num new_line" data-linenumber="812" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

812

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

<pre style="margin: 0;"> <span id="LC812" class="line" lang="python">                        <span class="n" style="color: #333;">num_matches</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="799" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

799

</td>

<td class="diff-line-num new_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

813

</td>

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

<pre style="margin: 0;"> <span id="LC813" class="line" lang="python">                        <span class="n" style="color: #333;">match_counts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">kmer_count</span><span class="p">)</span></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="800" 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">

800

</td>

<td class="diff-line-num new_line old" data-linenumber="814" 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="LC800" class="line" lang="python"><span class="idiff left right">                </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="801" style="width: 35px; color: rgba(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="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

814

</td>

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

<pre style="margin: 0;">+<span id="LC814" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="801" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

801

</td>

<td class="diff-line-num new_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

815

</td>

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

<pre style="margin: 0;"> <span id="LC815" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">num_matches</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="802" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

802

</td>

<td class="diff-line-num new_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

816

</td>

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

<pre style="margin: 0;"> <span id="LC816" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># not sure what the correct metric is to use here</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="803" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

803

</td>

<td class="diff-line-num new_line" data-linenumber="817" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

817

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

<pre style="margin: 0;"> <span id="LC817" class="line" lang="python">                    <span class="n" style="color: #333;">overall_count</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">match_counts</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">n_kmers</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="804" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

804

</td>

<td class="diff-line-num new_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

818

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

<pre style="margin: 0;"> <span id="LC818" class="line" lang="python">                    <span class="n" style="color: #333;">matches</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">Match</span><span class="p">(</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="805" 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">

805

</td>

<td class="diff-line-num new_line old" data-linenumber="819" 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="LC805" class="line" lang="python">                        <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">overall_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">tablesize</span><span class="p">),</span><span class="idiff left right"> </span></span>

</pre>

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</tr>

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

<td class="diff-line-num new old_line" data-linenumber="806" style="width: 35px; color: rgba(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="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

819

</td>

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

<pre style="margin: 0;">+<span id="LC819" class="line" lang="python">                        <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">overall_count</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">tablesize</span><span class="p">),</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

806

</td>

<td class="diff-line-num new_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

</td>

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

<pre style="margin: 0;"> <span id="LC820" class="line" lang="python">                        <span class="n" style="color: #333;">names</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">names</span><span class="p">,</span> <span class="n" style="color: #333;">match_frac</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">num_matches</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">n_kmers</span><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="807" 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">

807

</td>

<td class="diff-line-num new_line old" data-linenumber="821" 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="LC807" class="line" lang="python"><span class="idiff left right">            </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="808" style="width: 35px; color: rgba(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="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

821

</td>

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

<pre style="margin: 0;">+<span id="LC821" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="808" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

808

</td>

<td class="diff-line-num new_line" data-linenumber="822" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

822

</td>

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

<pre style="margin: 0;"> <span id="LC822" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Add remaining tags</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="809" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

809

</td>

<td class="diff-line-num new_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

823

</td>

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

<pre style="margin: 0;"> <span id="LC823" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tag</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">(</span><span class="n" style="color: #333;">candidates</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">())</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">seen</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="810" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

810

</td>

<td class="diff-line-num new_line" data-linenumber="824" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

824

</td>

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

<pre style="margin: 0;"> <span id="LC824" class="line" lang="python">                <span class="n" style="color: #333;">matches</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">Match</span><span class="p">(</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="811" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

811

</td>

<td class="diff-line-num new_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

825

</td>

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

<pre style="margin: 0;"> <span id="LC825" class="line" lang="python">                    <span class="n" style="color: #333;">tag</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">candidates</span><span class="p">[</span><span class="n" style="color: #333;">tag</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">tablesize</span><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="812" 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">

812

</td>

<td class="diff-line-num new_line old" data-linenumber="826" 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="LC812" class="line" lang="python"><span class="idiff left right">        </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="813" style="width: 35px; color: rgba(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="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

826

</td>

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

<pre style="margin: 0;">+<span id="LC826" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="813" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

813

</td>

<td class="diff-line-num new_line" data-linenumber="827" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

827

</td>

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

<pre style="margin: 0;"> <span id="LC827" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="814" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

814

</td>

<td class="diff-line-num new_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

828

</td>

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

<pre style="margin: 0;"> <span id="LC828" class="line" lang="python">            <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="815" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

815

</td>

<td class="diff-line-num new_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

829

</td>

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

<pre style="margin: 0;"> <span id="LC829" class="line" lang="python">                <span class="n" style="color: #333;">Match</span><span class="p">(</span><span class="n" style="color: #333;">tag</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">tablesize</span><span class="p">))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="816" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

816

</td>

<td class="diff-line-num new_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

830

</td>

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

<pre style="margin: 0;"> <span id="LC830" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tag</span><span class="p">,</span> <span class="n" style="color: #333;">count</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">candidates</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><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="817" 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">

817

</td>

<td class="diff-line-num new_line old" data-linenumber="831" 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="LC817" class="line" lang="python"><span class="idiff left right">        </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="818" style="width: 35px; color: rgba(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="831" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

831

</td>

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

<pre style="margin: 0;">+<span id="LC831" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="818" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

818

</td>

<td class="diff-line-num new_line" data-linenumber="832" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

832

</td>

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

<pre style="margin: 0;"> <span id="LC832" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">matches</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="819" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

819

</td>

<td class="diff-line-num new_line" data-linenumber="833" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

833

</td>

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

<pre style="margin: 0;"> <span id="LC833" 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="820" style="width: 35px; color: rgba(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="834" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

834

</td>

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

<pre style="margin: 0;">+<span id="LC834" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="820" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

820

</td>

<td class="diff-line-num new_line" data-linenumber="835" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

835

</td>

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

<pre style="margin: 0;"> <span id="LC835" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">align</span><span class="p">(</span><span class="n" style="color: #333;">seq1</span><span class="p">,</span> <span class="n" style="color: #333;">seq2</span><span class="p">,</span> <span class="n" style="color: #333;">min_overlap_frac</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.9</span><span class="p">):</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="821" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

821

</td>

<td class="diff-line-num new_line" data-linenumber="836" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

836

</td>

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

<pre style="margin: 0;"> <span id="LC836" class="line" lang="python">    <span class="s" style="color: #d14;">"""Align two sequences.</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="822" 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">

822

</td>

<td class="diff-line-num new_line old" data-linenumber="837" 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="LC822" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></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="823" style="width: 35px; color: rgba(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="837" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

837

</td>

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

<pre style="margin: 0;">+<span id="LC837" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="823" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

823

</td>

<td class="diff-line-num new_line" data-linenumber="838" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

838

</td>

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

<pre style="margin: 0;"> <span id="LC838" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</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="824" 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">

824

</td>

<td class="diff-line-num new_line old" data-linenumber="839" 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="LC824" class="line" lang="python"><span class="s" style="color: #d14;">        seq1, seq2: The sequences to align.</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="825" style="width: 35px; color: rgba(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="839" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

839

</td>

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

<pre style="margin: 0;">+<span id="LC839" class="line" lang="python"><span class="s" style="color: #d14;">        seq1: The second sequence to align.</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="825" style="width: 35px; color: rgba(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="840" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

840

</td>

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

<pre style="margin: 0;">+<span id="LC840" class="line" lang="python"><span class="s" style="color: #d14;">        seq2: The first sequence to align.</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="825" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

825

</td>

<td class="diff-line-num new_line" data-linenumber="841" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

841

</td>

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

<pre style="margin: 0;"> <span id="LC841" class="line" lang="python"><span class="s" style="color: #d14;">        min_overlap_frac: Minimum fraction of overlapping bases required for a</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="826" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

826

</td>

<td class="diff-line-num new_line" data-linenumber="842" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

842

</td>

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

<pre style="margin: 0;"> <span id="LC842" class="line" lang="python"><span class="s" style="color: #d14;">            match.</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="827" 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">

827

</td>

<td class="diff-line-num new_line old" data-linenumber="843" 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="LC827" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></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="828" style="width: 35px; color: rgba(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="843" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

843

</td>

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

<pre style="margin: 0;">+<span id="LC843" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="828" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

828

</td>

<td class="diff-line-num new_line" data-linenumber="844" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

844

</td>

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

<pre style="margin: 0;"> <span id="LC844" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="829" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

829

</td>

<td class="diff-line-num new_line" data-linenumber="845" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

845

</td>

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

<pre style="margin: 0;"> <span id="LC845" class="line" lang="python"><span class="s" style="color: #d14;">        The matching portion of the sequence.</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="830" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

830

</td>

<td class="diff-line-num new_line" data-linenumber="846" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

846

</td>

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

<pre style="margin: 0;"> <span id="LC846" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="df0576cbb783bc50b36e1efa3cbe0564a26c8295">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#df0576cbb783bc50b36e1efa3cbe0564a26c8295"><strong>doc/conf.py</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 @@ master_doc = 'index'</td>

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46

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<td class="diff-line-num 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">

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

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

</pre>

</td>

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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

</td>

<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># General information about the project.</span></span>

</pre>

</td>

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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">

48

</td>

<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">

48

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"><span class="n" style="color: #333;">project</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'atropos'</span></span>

</pre>

</td>

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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">

49

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'Original Cutadapt code: 2010-2014, Marcel Martin; Atropos modifications and improvements: 2015-201<span class="idiff left right">6</span>, John P Didion'</span></span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"><span class="n" style="color: #333;">copyright</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">u'Original Cutadapt code: 2010-2014, Marcel Martin; Atropos modifications and improvements: 2015-201<span class="idiff left right">8</span>, John P Didion'</span></span>

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

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The version info for the project you're documenting, acts as replacement for</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># |version| and |release|, also used in various other places throughout the</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="208" style="width: 35px; color: rgba(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">@@ -208,8 +208,7 @@ latex_elements = {</td>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># (source start file, target name, title,</span></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#  author, documentclass [howto, manual, or own class]).</span></span>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python"><span class="n" style="color: #333;">latex_documents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python">  <span class="p">(</span><span class="s" style="color: #d14;">'index'</span><span class="p">,</span> <span class="s" style="color: #d14;">'atropos.tex'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'atropos Documentation'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="python">   <span class="s" style="color: #d14;">u'Marcel Martin'</span><span class="p">,</span> <span class="s" style="color: #d14;">'manual'</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python">  <span class="p">(</span><span class="s" style="color: #d14;">'index'</span><span class="p">,</span> <span class="s" style="color: #d14;">'atropos.tex'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'Atropos Documentation'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'John Didion'</span><span class="p">,</span> <span class="s" style="color: #d14;">'manual'</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The name of an image file (relative to this directory) to place at the top of</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="237" style="width: 35px; color: rgba(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">@@ -238,8 +237,7 @@ latex_documents = [</td>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># One entry per manual page. List of tuples</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># (source start file, name, description, authors, manual section).</span></span>

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

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<pre style="margin: 0;">-<span id="LC241" class="line" lang="python">    <span class="p">(</span><span class="s" style="color: #d14;">'index'</span><span class="p">,</span> <span class="s" style="color: #d14;">'atropos'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'atropos Documentation'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC242" class="line" lang="python">     <span class="p">[</span><span class="s" style="color: #d14;">u'Marcel Martin'</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python">    <span class="p">(</span><span class="s" style="color: #d14;">'index'</span><span class="p">,</span> <span class="s" style="color: #d14;">'atropos'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'Atropos Documentation'</span><span class="p">,</span> <span class="p">[</span><span class="s" style="color: #d14;">u'John Didion'</span><span class="p">],</span> <span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># If true, show URL addresses after external links.</span></span>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -252,9 +250,8 @@ man_pages = [</td>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># (source start file, target name, title, author,</span></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#  dir menu entry, description, category)</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"><span class="n" style="color: #333;">texinfo_documents</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python">  <span class="p">(</span><span class="s" style="color: #d14;">'index'</span><span class="p">,</span> <span class="s" style="color: #d14;">'atropos'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'atropos Documentation'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="python">   <span class="s" style="color: #d14;">u'Marcel Martin'</span><span class="p">,</span> <span class="s" style="color: #d14;">'atropos'</span><span class="p">,</span> <span class="s" style="color: #d14;">'One line description of project.'</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="python">   <span class="s" style="color: #d14;">'Miscellaneous'</span><span class="p">),</span></span>

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

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<td class="diff-line-num new new_line" data-linenumber="253" style="width: 35px; color: rgba(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="LC253" class="line" lang="python">  <span class="p">(</span><span class="s" style="color: #d14;">'index'</span><span class="p">,</span> <span class="s" style="color: #d14;">'atropos'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'atropos Documentation'</span><span class="p">,</span> <span class="s" style="color: #d14;">u'John Didion'</span><span class="p">,</span> <span class="s" style="color: #d14;">'atropos'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="254" style="width: 35px; color: rgba(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="LC254" class="line" lang="python">   <span class="s" style="color: #d14;">'General purpose NGS read manipulation tool.'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Read manipulation'</span><span class="p">),</span></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="260" style="width: 35px; color: rgba(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="LC257" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Documents to append as an appendix to all manuals.</span></span>

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<br>

</li>

<li id="ee1d7278a009e2c5c652622fe43dc77e39af740d">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#ee1d7278a009e2c5c652622fe43dc77e39af740d"><strong>doc/guide.rst</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="657" style="width: 35px; color: rgba(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="657" style="width: 35px; color: rgba(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">@@ -657,10 +657,10 @@ been removed. For example, if the following sequence is in reads.fastq::</td>

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="plaintext">    ACGTACGTACGTADAP</span>

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<pre style="margin: 0;"> <span id="LC658" class="line" lang="plaintext"></span>

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659

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<pre style="margin: 0;"> <span id="LC659" class="line" lang="plaintext">The following command will first trim the ``ADAP`` part of the adapter</span>

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<td class="diff-line-num new_line old" data-linenumber="660" 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="LC660" class="line" lang="plaintext">off the end. Then, since only 4 bases were trimmed, the ``-i 5`` option</span>

</pre>

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<pre style="margin: 0;">+<span id="LC660" class="line" lang="plaintext">off the end. Then, since only 4 bases were trimmed, the ``-i <span class="idiff left right">-</span>5`` option</span>

</pre>

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661

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<td class="diff-line-num new_line" data-linenumber="661" style="width: 35px; color: rgba(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="LC661" class="line" lang="plaintext">will cause a 5th base to be removed.</span>

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC663" class="line" lang="plaintext">    atropos -A ADAPTER -i 5 -o trimmed.fastq -se reads.fastq</span>

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<pre style="margin: 0;">+<span id="LC663" class="line" lang="plaintext">    atropos -A ADAPTER -i <span class="idiff left right">-</span>5 -o trimmed.fastq -se reads.fastq</span>

</pre>

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<pre style="margin: 0;"> <span id="LC664" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="plaintext">.. _quality-trimming:</span>

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<pre style="margin: 0;"> <span id="LC666" class="line" lang="plaintext"></span>

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<li id="1bbcd8980c541f52998ccf56da078edd2ca6a2d0">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#1bbcd8980c541f52998ccf56da078edd2ca6a2d0"><strong>doc/index.rst</strong></a>

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

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

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

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Table of contents</span>

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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="plaintext">=================</span>

</pre>

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</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/atropos/compare/c903af9bf83e294c37a75f5eb3c4a06e38c1e2cd...dbfa561b04043199fbaf24ea48f33f0e88285651#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="146" style="width: 35px; color: rgba(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="146" style="width: 35px; color: rgba(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">@@ -146,7 +146,7 @@ setup(</td>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python">    <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"https://atropos.readthedocs.org/"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python">    <span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"trim adapters from high-throughput sequencing reads"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python">    <span class="n" style="color: #333;">long_description</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">long_description</span><span class="p">,</span></span>

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="python">    <span class="n" style="color: #333;">log_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"text/markdown"</span><span class="p">,</span></span>

</pre>

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149

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python">    <span class="n" style="color: #333;">lo<span class="idiff left right">n</span>g_description_content_type</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"text/markdown"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

150

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150

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python">    <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Original Cutadapt code is under MIT license; improvements and additions are in the Public Domain"</span><span class="p">,</span></span>

</pre>

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151

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151

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python">    <span class="n" style="color: #333;">ext_modules</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extensions</span><span class="p">,</span></span>

</pre>

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152

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python">    <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">find_packages</span><span class="p">(),</span></span>

</pre>

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