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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/879e6a06365e1352226a649e6d979e1ce87f23f5">879e6a06</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2019-11-30T12:00:22Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.1.24+dfsg</pre>

</li>

</ul>

<h4>10 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<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="#e8f677b53615a7ffaf54ba5416957562ba27e685">

atropos/commands/legacy_report.py

</a>

</li>

<li class="file-stats">

<a href="#f88c7193047348563d4cfabf2ec77be4c615e6e7">

atropos/io/seqio.py

</a>

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<li class="file-stats">

<a href="#1fb9116d8cf0c1b4d5121d2b653391d84b794ac6">

atropos/util/__init__.py

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<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

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</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">python</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">cache</span><span class="pi">:</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml">  <span class="na" style="color: #008080;">directories</span><span class="pi">:</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">$HOME/.cache/pip"</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">python</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">3.4.3</span></span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"><span class="pi">-</span> <span class="m" style="color: #099;">3.5</span></span>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml"><span class="pi">-</span> <span class="m" style="color: #099;">3.6</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml">  <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">python</span><span class="pi">:</span> <span class="m" style="color: #099;">3.7</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml">      <span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">xenial</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml">      <span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">true</span></span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.4.5"</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.5"</span></span>

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</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.6"</span></span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.7"</span></span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml">  <span class="pi">-</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">3.8"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml"><span class="na" style="color: #008080;">install</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install --upgrade pip wheel</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="yaml"><span class="pi">-</span> <span class="s" style="color: #d14;">pip install Cython</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">

<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.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_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

</td>

<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

</td>

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

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="gh" style="color: #999;">v1.1.22 (dev)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC4" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------</span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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

</td>

<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">v1.1.24 (2019.11.27)</span>

</pre>

</td>

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<td class="diff-line-num new old_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">

</td>

<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

</td>

<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>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_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">

</td>

<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

</td>

<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> Fix #87 - Python 3.8 compatibility, time.clock removed</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="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">

</td>

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

6

</td>

<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>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<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

</td>

<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">v1.1.23 (2019.11.22)</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> Set minimum Python version to 3.4.5</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">*</span> Fixed #86 - no trimming performed for single-end BAM file</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_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">

</td>

<td class="diff-line-num new new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

</td>

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">v1.1.22 (2019.05.20)</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="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">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

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

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

</pre>

</td>

</tr>

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

<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

</td>

<td class="diff-line-num new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

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

<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown"><span class="p">*</span> Documentation fixes (#79)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

</td>

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="markdown"><span class="p">*</span> Fix for index error when running <span class="sb" style="color: #d14;">`detect`</span> command (#80)</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

</td>

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="markdown"></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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

</td>

<td class="diff-line-num new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

</td>

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

<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown">v1.1.21 (2018.11.24)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">--------------------</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown"></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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

</td>

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

<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="p">*</span> Added long options for paired adapter parameters.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

11

</td>

<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

</td>

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

<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="diff-line-num new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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

<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown">v1.1.20 (2018.11.21)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<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">

</td>

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">--------------------</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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

</td>

<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="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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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">

23

</td>

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

<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="p">*</span> Fix #74: Make pysam open SAM/BAM files with check_sq=False by default</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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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">

24

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

<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"><span class="p">*</span> Fixed setup.py to correctly include README for PyPI.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

</td>

<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">

25

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

26

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

<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown">v1.1.19 (2018.05.16)</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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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

</td>

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="markdown"><span class="gh" style="color: #999;"><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="19" style="width: 35px; color: rgba(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="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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

<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="p">*</span> Fix #68: Error when using insert aligner with adapters of different lengths</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

</td>

<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

21

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

30

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

<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown">v1.1.18 (2018.03.16)</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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

22

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="gh" style="color: #999;"><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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

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

</pre>

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p">*</span> Added two new tools to the benchmarks:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"><span class="p">  *</span> fastp</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"><span class="p">  *</span> Cutadapt</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="36" style="width: 35px; color: rgba(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">@@ -27,78 +36,78 @@ v1.1.18 (2018.03.16)</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="markdown"><span class="p">*</span> Fix #64: InsertAligner not respecting match_adapter_wildcards and match_read_wildcards options.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown">v1.1.17 (2018.01.13)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">--------------------</span></span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); 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="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown"><span class="p">*</span> Fix #51: Reads of different lengths not error corrected.</span>

</pre>

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown">v1.1.16 (2018.01.07)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">--------------------</span></span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC43" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); 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="44" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC44" class="line" lang="markdown"><span class="p">*</span> Fix for #57: LegacyReport stops on adapter with no trimmed reads, and LegacyReport errors when histogram data is None. Thanks to @cokelaer and @pyMyt1!</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC45" class="line" lang="markdown"><span class="p">*</span> Fix for #58: NextSeqTrimmer not trimming from both ends. Thanks to @pkMyt1!</span>

</pre>

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

</pre>

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<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">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown">v1.1.15 (2017.09.28)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(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="LC39" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">--------------------</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); 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="48" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC48" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"><span class="p">*</span> Fix for #41: Error when using progress bar.</span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC50" class="line" lang="markdown"><span class="p">*</span> Fix for #42: Discordance between Cutadapt and Atropos in number of expected events.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

</td>

<td class="diff-line-num 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">

51

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"><span class="p">*</span> Added '--alphabet' option. Set to 'dna' to validate input sequences against the allowed DNA characters (A/C/G/T/N). This fixes #43 and partially fixes #44.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

</td>

<td class="diff-line-num new_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">

52

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

<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"><span class="p">*</span> Fixed #44: Uncaught errors not being logged.</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="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

44

</td>

<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

53

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

<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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

<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown">v1.1.14 (2017.09.19)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

46

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<td class="diff-line-num new_line old" data-linenumber="55" style="width: 35px; color: rgba(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="LC46" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">--------------------</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="47" style="width: 35px; color: rgba(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="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">

55

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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="LC55" class="line" lang="markdown"></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

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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">

56

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

<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"><span class="p">*</span> Fix for #39: miRNA option error (thanks to @mottodora)</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="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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<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">

57

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

<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"><span class="p">*</span> Fix for #37: fixes overflow error when computing RandomMatchProbability on long reads (>150 bp)</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="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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<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">

58

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

<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"></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="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

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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="markdown">v1.1.13 (2017.09.14)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

51

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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">

</td>

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

<pre style="margin: 0;">-<span id="LC51" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left 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="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<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">

60

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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="markdown"></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="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">

52

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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

<pre style="margin: 0;"> <span id="LC61" class="line" lang="markdown"><span class="p">*</span> Fix for #38: Atropos fails with MultiCore error when using OrderPreservingWriterResultsHandler (thanks to @cshenanigans)</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="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">

53

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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">

62

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

<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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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">

63

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

<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown">v1.1.12 (2017.08.15)</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="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

55

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<td class="diff-line-num new_line old" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC55" class="line" lang="markdown"><span class="gh" style="color: #999;"><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="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_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">

64

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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="LC64" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

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

56

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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">

65

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

<pre style="margin: 0;"> <span id="LC65" class="line" lang="markdown"><span class="p">*</span> Expose --min-frequency and --min-contaminant-match-frac options to 'detect -d heuristic' command.</span>

</pre>

</td>

</tr>

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

<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">

57

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

66

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

<pre style="margin: 0;"> <span id="LC66" class="line" lang="markdown"><span class="p">*</span> Expose --min-kmer-match-frac option to 'detect -d known' command.</span>

</pre>

</td>

</tr>

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

<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="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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

<pre style="margin: 0;"> <span id="LC67" class="line" lang="markdown"><span class="p">*</span> Fixed #35: using incorrect metric to determine match fraction in 'detect -d known' command.</span>

</pre>

</td>

</tr>

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

<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="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

68

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

<pre style="margin: 0;"> <span id="LC68" class="line" lang="markdown"></span>

</pre>

</td>

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60

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<td class="diff-line-num new_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">

69

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

<pre style="margin: 0;"> <span id="LC69" class="line" lang="markdown">v1.1.11 (2017.08.15)</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="70" style="width: 35px; color: rgba(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="LC61" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">--------------------</span></span></span>

</pre>

</td>

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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="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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

<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"></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="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">

71

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="markdown"><span class="p">*</span> Fixed #34: JSON report output not working with SRA streaming.</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="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

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

<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>

</pre>

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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="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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

<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown">v1.1.10 (2017.08.09)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

65

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<td class="diff-line-num new_line old" data-linenumber="74" style="width: 35px; color: rgba(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="LC65" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">--------------------</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

74

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

<pre style="margin: 0;">+<span id="LC74" class="line" lang="markdown"></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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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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

<pre style="margin: 0;"> <span id="LC75" class="line" lang="markdown"><span class="p">*</span> Improve debugging messages</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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

76

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

<pre style="margin: 0;"> <span id="LC76" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

77

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

<pre style="margin: 0;"> <span id="LC77" class="line" lang="markdown">v1.1.9 (2017.08.01)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(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="78" style="width: 35px; color: rgba(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="LC69" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">-------------------</span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC78" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); 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="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

79

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

<pre style="margin: 0;"> <span id="LC79" class="line" lang="markdown"><span class="p">*</span> Fix #30: failure when using --preserve-order option</span>

</pre>

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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">

71

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<td class="diff-line-num new_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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

<pre style="margin: 0;"> <span id="LC80" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

72

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<td class="diff-line-num new_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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

<pre style="margin: 0;"> <span id="LC81" class="line" lang="markdown">v1.1.8 (2017.07.10)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

73

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<td class="diff-line-num new_line old" data-linenumber="82" style="width: 35px; color: rgba(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="LC73" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">-------------------</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

82

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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="LC82" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

74

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<td class="diff-line-num new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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

<pre style="margin: 0;"> <span id="LC83" class="line" lang="markdown"><span class="p">*</span> Add --config option for specifying options in a config file.</span>

</pre>

</td>

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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">

75

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<td class="diff-line-num new_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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

<pre style="margin: 0;"> <span id="LC84" class="line" lang="markdown"><span class="p">*</span> Fix for #29: allow paired-end quality and N trimming without adapter trimming.</span>

</pre>

</td>

</tr>

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

<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">

76

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<td class="diff-line-num new_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

85

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

<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"><span class="p">*</span> Removed twine register command from make release</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

77

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<td class="diff-line-num new_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

86

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

<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"></span>

</pre>

</td>

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78

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown">v1.1.7 (2017.06.01)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

79

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<td class="diff-line-num new_line old" data-linenumber="88" style="width: 35px; color: rgba(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="LC79" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">-------------------</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); 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="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

88

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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="LC88" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="80" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

80

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<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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

<pre style="margin: 0;"> <span id="LC89" class="line" lang="markdown"><span class="p">*</span> Stream reads directly from an SRA accession for any atropos command using the</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

81

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<td class="diff-line-num new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

90

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

<pre style="margin: 0;"> <span id="LC90" class="line" lang="markdown">  -sra option.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="82" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

82

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<td class="diff-line-num new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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

<pre style="margin: 0;"> <span id="LC91" class="line" lang="markdown"><span class="p">*</span> Add detect option to specify the bases that signify when the sequencer has</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

83

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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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

<pre style="margin: 0;"> <span id="LC92" class="line" lang="markdown">  read past the end of a fragment.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

84

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

85

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<td class="diff-line-num new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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

<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown">v1.1.6 (2017.05.30)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

86

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

<pre style="margin: 0;">-<span id="LC86" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">-------------------</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); 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">

95

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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="LC95" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

87

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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">

96

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"><span class="p">*</span> Add FASTA output for detect command, and enable json, yaml, and pickle output for all commands.</span>

</pre>

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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="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">

97

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

<pre style="margin: 0;"> <span id="LC97" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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

98

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

<pre style="margin: 0;"> <span id="LC98" class="line" lang="markdown">v1.1.5 (2017.05.18)</span>

</pre>

</td>

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90

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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">

</td>

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

<pre style="margin: 0;">-<span id="LC90" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">-------------------</span></span></span>

</pre>

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

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

99

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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="LC99" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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<td class="diff-line-num new_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

100

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

<pre style="margin: 0;"> <span id="LC100" class="line" lang="markdown"><span class="p">*</span> Major update to the documentation.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

101

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

<pre style="margin: 0;"> <span id="LC101" class="line" lang="markdown"><span class="p">*</span> Fixed error messages in multi-threaded mode.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

93

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

102

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

<pre style="margin: 0;"> <span id="LC102" class="line" lang="markdown"><span class="p">*</span> Fixed bug when generating reports for runs involving error correction.</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

94

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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">

103

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

<pre style="margin: 0;"> <span id="LC103" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

95

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<td class="diff-line-num new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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

<pre style="margin: 0;"> <span id="LC104" class="line" lang="markdown">v1.1.4 (2017.05.02)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

96

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<td class="diff-line-num new_line old" data-linenumber="105" style="width: 35px; color: rgba(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="LC96" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">-------------------</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

97

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

106

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="markdown"><span class="p">*</span> Exposed option to set PRNG seed when subsampling reads.</span>

</pre>

</td>

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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">

98

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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="markdown"><span class="p">*</span> Fixed issue #14: 'detect' and 'error' commands were broken. This involved rewriting those commands to use the same pipeline and reporting frameworks as the 'trim' and 'qc' commands.</span>

</pre>

</td>

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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">

99

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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

100

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="markdown">v1.1.3 (2017.05.01)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

101

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<td class="diff-line-num new_line old" data-linenumber="110" style="width: 35px; color: rgba(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="LC101" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">-------------------</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="102" style="width: 35px; color: rgba(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="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC110" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_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">

102

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<td class="diff-line-num new_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="markdown"><span class="p">*</span> Updated Dockerfile to use smaller, Alpine-based image.</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="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">

103

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<td class="diff-line-num new_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

112

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="markdown"><span class="p">*</span> Added Docker image for v1.1.2 to Docker Hub.</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="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

104

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<td class="diff-line-num new_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

113

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<pre style="margin: 0;"> <span id="LC113" class="line" lang="markdown"><span class="p">*</span> Updated Travis config to automatically build Docker images for each release.</span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -107,7 +116,6 @@ v1.1.3 (2017.05.01)</td>

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

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<td class="diff-line-num new_line" data-linenumber="116" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC116" class="line" lang="markdown"><span class="p">*</span> Fixed #13: unnecessary differences in summary output between Cutadapt and Atropos.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

108

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<td class="diff-line-num new_line" data-linenumber="117" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

117

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

<pre style="margin: 0;"> <span id="LC117" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

118

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="markdown">v1.1.2 (2017.04.12)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

110

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<td class="diff-line-num new_line old" data-linenumber="119" style="width: 35px; color: rgba(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="LC110" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------</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="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="diff-line-num new_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

119

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

120

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="markdown"><span class="p">*</span> New 'qc' command computes read-level statistics.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

113

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<td class="diff-line-num new_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="markdown"><span class="p">*</span> The 'trim' command can also compute read-level statistic pre- and/or post-trimming using the new '--stats' option.</span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -125,7 +133,6 @@ v1.1.2 (2017.04.12)</td>

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<td class="diff-line-num old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="markdown"><span class="p">*</span> Ported some recent enhancments over from Cutadapt.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); 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="134" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC134" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC135" class="line" lang="markdown">v1.0.23 (2016.12.07)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC128" 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="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="LC136" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); 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="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> Identified a subtle bug having to do with insufficient memory in multi-threaded mode. The main thread appears to hang waiting for the next read from the input file. This appears to occur only under a strictly-regulated memory cap such as on cluster environment. This bug is not fixed, but I added the following:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="markdown"><span class="p">    *</span> Set the default batch size based on the queue sizes</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -133,36 +140,30 @@ v1.0.23 (2016.12.07)</td>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="markdown"><span class="p">*</span> Bug fixes</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="markdown">v1.0.22 (2016.12.02)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="markdown"></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">

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC144" class="line" lang="markdown"><span class="p">*</span> Abstracted the ErrorEstimator class to enable alternate implementations.</span>

</pre>

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

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC145" class="line" lang="markdown"><span class="p">*</span> Added a new ShadowRegressionErrorEstimator that uses the ShadowRegression R package (Wang et al.) to more accurately estimate sequencing error rate. This requires that R and the <span class="p">[</span><span class="nv" style="color: #008080;">ShadowRegression package</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bcb.dfci.harvard.edu/~vwang/shadowRegression.html</span><span class="p">)</span> and its dependencies be installed -- MASS and ReadCount, which in turn depend on a bunch of Bioconductor packages. At some point, this dependency will go away when I reimplement the method in pure python.</span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="markdown"><span class="p">*</span> The error command now reports the longest matching read fragment, which is usually a closer match for the actual adapter sequence than the longest matching k-mer.</span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC147" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); 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">

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="markdown">v1.0.21 (2016.11.23)</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">

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<pre style="margin: 0;">-<span id="LC143" 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="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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<td class="diff-line-num new_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC149" class="line" lang="markdown"></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="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="markdown"><span class="p">*</span> Bugfixes</span>

</pre>

</td>

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<td class="diff-line-num 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">

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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">

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="markdown"></span>

</pre>

</td>

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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="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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<pre style="margin: 0;"> <span id="LC152" class="line" lang="markdown">v1.0.20 (2016.11.22)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" 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="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

149

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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">

153

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="markdown"></span>

</pre>

</td>

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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

</td>

<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">

154

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="markdown"><span class="p">*</span> Changed the order of trimming operations - OverwriteReadModifier is now after read and quality trimming.</span>

</pre>

</td>

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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">

151

</td>

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

<pre style="margin: 0;"> <span id="LC155" class="line" lang="markdown"><span class="p">*</span> Refactored the main Atropos interface to improve testability.</span>

</pre>

</td>

</tr>

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

<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">

152

</td>

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

<pre style="margin: 0;"> <span id="LC156" class="line" lang="markdown"><span class="p">*</span> Added more unit tests.</span>

</pre>

</td>

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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">

153

</td>

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

<pre style="margin: 0;"> <span id="LC157" class="line" lang="markdown"></span>

</pre>

</td>

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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">

154

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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">

158

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<pre style="margin: 0;"> <span id="LC158" class="line" lang="markdown">v1.0.19 (2016.11.21)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

155

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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">

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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="LC155" 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="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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<td class="diff-line-num new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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

<pre style="margin: 0;"> <span id="LC159" class="line" lang="markdown"></span>

</pre>

</td>

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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">

157

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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="markdown"><span class="p">*</span> Fixed a major bug in OverwriteReadModifier, and in the unit tests for paired-end trimmers.</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="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">

158

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

<pre style="margin: 0;"> <span id="LC161" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

159

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<td class="diff-line-num new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

162

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

<pre style="margin: 0;"> <span id="LC162" class="line" lang="markdown">v1.0.18 (2016.11.20)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

160

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<td class="diff-line-num new_line old" data-linenumber="163" style="width: 35px; color: rgba(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="LC160" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>

</pre>

</td>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

163

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

<pre style="margin: 0;"> <span id="LC163" class="line" lang="markdown"></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="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

162

</td>

<td class="diff-line-num new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

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

<pre style="margin: 0;"> <span id="LC164" class="line" lang="markdown"><span class="p">*</span> Added OverwriteReadModifier, a paired-end modifier that overwrites one read end with the other if the mean quality over the first N bases (where N is user-specified) of one is below a threshold value and the mean quality of the other is above a second threshold. This dramatically improves the number of high-quality read mappings in data sets where there are systematic problems with one read-end.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

163

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<td class="diff-line-num new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

165

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

<pre style="margin: 0;"> <span id="LC165" class="line" lang="markdown"></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="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

164

</td>

<td class="diff-line-num new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

166

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

<pre style="margin: 0;"> <span id="LC166" class="line" lang="markdown">v1.0.17 (2016.11.18)</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="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

165

</td>

<td class="diff-line-num new_line old" data-linenumber="167" style="width: 35px; color: rgba(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="LC165" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

166

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<td class="diff-line-num new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

167

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

<pre style="margin: 0;"> <span id="LC167" class="line" lang="markdown"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

167

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<td class="diff-line-num new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

168

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="markdown"><span class="p">*</span> Perform error correction when insert match fails but adapter matches are complementary</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

168

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<td class="diff-line-num new_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">

169

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

<pre style="margin: 0;"> <span id="LC169" class="line" lang="markdown"><span class="p">*</span> Improvements to handling of cached adapter lists</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold 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">...</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">@@ -171,7 +172,6 @@ v1.0.17 (2016.11.18)</td>

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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">

171

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<td class="diff-line-num 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">

172

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<pre style="margin: 0;"> <span id="LC172" class="line" lang="markdown"><span class="p">*</span> Many</span>

</pre>

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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 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">v1.0.16 (2016.09.20)</span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="175" style="width: 35px; color: rgba(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="LC174" 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="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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<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="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">

176

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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> Migrate to Versioneer for version management.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC177" class="line" lang="markdown"><span class="p">*</span> Enable stderr as a valid output using the '<span class="se" style="color: #d14;">\_</span>' shortcut.</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="182" style="width: 35px; color: rgba(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="182" style="width: 35px; color: rgba(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">@@ -182,14 +182,12 @@ v1.0.16 (2016.09.20)</td>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="markdown"><span class="p">*</span> When InsertAdapterCutter.symmetric is True and mismatch_action is not None, insert match fails, at least one adapter match succeeds, and the adapter matches (if there are two) are complementary, then the reads are treated as overlapping and error correction is performed. This leads to substantial improvements when one read is of good quality while the other is other is of poor quality.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC184" class="line" lang="markdown">v1.0.15 (2016.09.14)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); 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="186" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC186" class="line" lang="markdown"><span class="p">*</span> Fixed missing import bug in 'detect' command.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC187" class="line" lang="markdown"><span class="p">*</span> Added estimate of fraction of contaminated reads to output of 'detect' command.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

189

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<td class="diff-line-num new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="markdown"><span class="p">*</span> Optionally cache list of known contaminants rather than re-download it every time.</span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC189" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="markdown">v1.0.14 (2016.09.13)</span>

</pre>

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192

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

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<pre style="margin: 0;">-<span id="LC192" 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="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">

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<td class="diff-line-num new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC191" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); 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="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="markdown"><span class="p">*</span> Implemented <span class="se" style="color: #d14;">\_</span>align.MultiAligner, which returns all matches that satisfy the overlap and error thresholds. align.InsertAligner now uses MultiAligner for insert matching, and tests all matches in decreasing size order until it finds one with adapter matches (if any).</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="markdown"><span class="p">*</span> Major improvements to the accuracy of the 'detect' command.</span>

</pre>

</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">@@ -201,62 +199,52 @@ v1.0.14 (2016.09.13)</td>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="markdown"><span class="p">*</span> Sevaral other bugfixes.</span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="markdown">v1.0.13 (2016.08.31)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); 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="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC203" class="line" lang="markdown"><span class="p">*</span> Add options to specify max error rates for insert and adapter matching within insert aligner.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="markdown"><span class="p">*</span> Add new command to estimate empirical error rate in data set from base qualities.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); 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="206" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC206" class="line" lang="markdown">v1.0.12 (2016.08.30)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>

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

</pre>

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<td class="diff-line-num 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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="markdown"><span class="p">*</span> Add ability to correct errors during insert-match adapter trimming.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); 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="209" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC209" class="line" lang="markdown"><span class="p">*</span> Implement additional adapter-detection algorithms.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="markdown"><span class="p">*</span> Fix bug where default output file is force-created in parallel-write mode</span>

</pre>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="markdown">v1.0.11 (2016.08.24)</span>

</pre>

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<pre style="margin: 0;">-<span id="LC217" 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="218" style="width: 35px; color: rgba(0,0,0,0.3); 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="213" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC213" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); 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="214" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC214" class="line" lang="markdown"><span class="p">*</span> Clarify and fix issues with bisulfite trimming. Notably, rrbs and non-directional are now allowed independently or in combination.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC215" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); 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="216" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC216" class="line" lang="markdown">v1.0.10 (2016.08.23)</span>

</pre>

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222

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<td class="diff-line-num new_line old" data-linenumber="217" style="width: 35px; color: rgba(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="LC222" class="line" lang="markdown"><span class="gh" style="color: #999;">--------------------</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

223

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<td class="diff-line-num new_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

217

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

<pre style="margin: 0;"> <span id="LC217" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num 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">

224

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<td class="diff-line-num new_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

218

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

<pre style="margin: 0;"> <span id="LC218" class="line" lang="markdown"><span class="p">*</span> Introduced new 'detect' command for automatically detecting adapter sequences.</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="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

225

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<td class="diff-line-num new_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

219

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

<pre style="margin: 0;"> <span id="LC219" class="line" lang="markdown"><span class="p">*</span> Options are now required to specify input files.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

226

</td>

<td class="diff-line-num new_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

220

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

<pre style="margin: 0;"> <span id="LC220" class="line" lang="markdown"><span class="p">*</span> Major updates to documentation.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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">

227

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<td class="diff-line-num new_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

221

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

<pre style="margin: 0;"> <span id="LC221" class="line" lang="markdown"></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="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

228

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<td class="diff-line-num new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

222

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

<pre style="margin: 0;"> <span id="LC222" class="line" lang="markdown">v1.0.9 (2016.08.22)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

229

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<td class="diff-line-num new_line old" data-linenumber="223" style="width: 35px; color: rgba(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="LC229" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); 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="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

223

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

<pre style="margin: 0;"> <span id="LC223" class="line" lang="markdown"></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="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

231

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<td class="diff-line-num new_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">

224

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

<pre style="margin: 0;"> <span id="LC224" class="line" lang="markdown"><span class="p">*</span> Bugfix release</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="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

232

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<td class="diff-line-num new_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

225

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

<pre style="margin: 0;"> <span id="LC225" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

233

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<td class="diff-line-num new_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

226

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

<pre style="margin: 0;"> <span id="LC226" class="line" lang="markdown">v1.0.8 (2016.08.19)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

234

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<td class="diff-line-num new_line old" data-linenumber="227" style="width: 35px; color: rgba(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="LC234" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

235

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<td class="diff-line-num 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">

227

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

<pre style="margin: 0;"> <span id="LC227" class="line" lang="markdown"></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="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

236

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<td class="diff-line-num new_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

228

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

<pre style="margin: 0;"> <span id="LC228" class="line" lang="markdown"><span class="p">*</span> Reverted previously introduced (and no longer necessary) dependency on bitarray).</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_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">

237

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<td class="diff-line-num new_line" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

229

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

<pre style="margin: 0;"> <span id="LC229" class="line" lang="markdown"><span class="p">*</span> Switched the insert aligner back to the default implementation, as the one that ignores indels is not any faster.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

238

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<td class="diff-line-num new_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

230

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

239

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<td class="diff-line-num new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

231

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

<pre style="margin: 0;"> <span id="LC231" class="line" lang="markdown">v1.0.7 (2016.08.18)</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="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

240

</td>

<td class="diff-line-num new_line old" data-linenumber="232" style="width: 35px; color: rgba(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="LC240" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

241

</td>

<td class="diff-line-num new_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

232

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

242

</td>

<td class="diff-line-num new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

233

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

<pre style="margin: 0;"> <span id="LC233" class="line" lang="markdown"><span class="p">*</span> Re-engineered modifiers.py (and all dependent code) to enable use of modifiers that simultaneously edit both reads in a pair.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

243

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<td class="diff-line-num new_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

234

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

<pre style="margin: 0;"> <span id="LC234" class="line" lang="markdown"><span class="p">*</span> Add --op-order option to enable use to specify order of first four trimming operations.</span>

</pre>

</td>

</tr>

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<td class="diff-line-num old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); 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="235" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC235" class="line" lang="markdown"><span class="p">*</span> Implemented insert-based alignment for paired-end adapter trimming. This is currently experimental. Benchmarking against SeqPurge and Skewer using simulated reads showed that the method Cutadapt uses to align adapters, while optimal for single-end reads, is much less sensitive and specific than the insert match algorithms used by SeqPurge and Skewer. Our algorithm is similar to the one used by SeqPurge but leverages the dynamic programming model of Cutadapt.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

245

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<td class="diff-line-num new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

236

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

246

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<td class="diff-line-num 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">

237

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="markdown">v1.0.6 (2016.08.08)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

247

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<td class="diff-line-num new_line old" data-linenumber="238" style="width: 35px; color: rgba(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="LC247" 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="248" style="width: 35px; color: rgba(0,0,0,0.3); 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="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

238

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); 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="239" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC239" class="line" lang="markdown"><span class="p">*</span> Based on tests, worker compression is faster than writer compression when more than 8 threads are available, so set this to be the default.</span>

</pre>

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<td class="diff-line-num old_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">

250

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<td class="diff-line-num new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

240

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

<pre style="margin: 0;"> <span id="LC240" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

251

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<td class="diff-line-num new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

241

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="markdown">v1.0.5 (2016.08.06)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

252

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<td class="diff-line-num new_line old" data-linenumber="242" style="width: 35px; color: rgba(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="LC252" 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="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

253

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<td class="diff-line-num new_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

242

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="254" style="width: 35px; color: rgba(0,0,0,0.3); 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="243" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC243" class="line" lang="markdown"><span class="p">*</span> Interanal code reorganization - compression code moved to separate module</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

255

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<td class="diff-line-num new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC244" class="line" lang="markdown"><span class="p">*</span> Eliminated the --worker-compression option in favor of --compression (whose value is either 'worker' or 'writer')</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); 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="245" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC245" class="line" lang="markdown"><span class="p">*</span> More documentation improvements</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); 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="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

246

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); 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="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

247

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="markdown">v1.0.3 (2016.08.05)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="259" style="width: 35px; color: rgba(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="248" style="width: 35px; color: rgba(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="LC259" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------</span></span>

</pre>

</td>

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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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<td class="diff-line-num new_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC248" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); 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="249" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC249" class="line" lang="markdown"><span class="p">*</span> Significant performance improvements:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="markdown"><span class="p">    *</span> Start an extra worker once the main process is finished loading reads</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="267" style="width: 35px; color: rgba(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="255" style="width: 35px; color: rgba(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">@@ -267,12 +255,11 @@ v1.0.3 (2016.08.05)</td>

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<td class="diff-line-num old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); 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="255" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC255" class="line" lang="markdown"><span class="p">*</span> Eliminated the --parallel-environment option</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); 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="256" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC256" class="line" lang="markdown"></span>

</pre>

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269

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<td class="diff-line-num new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

257

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

<pre style="margin: 0;"> <span id="LC257" class="line" lang="markdown">v1.0.1 (2016.08.04)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

270

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<td class="diff-line-num new_line old" data-linenumber="258" style="width: 35px; color: rgba(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="LC270" class="line" lang="markdown"><span class="gh" style="color: #999;">-------------------</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

271

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<td class="diff-line-num new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

258

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

272

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<td class="diff-line-num new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

259

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="markdown"><span class="p">*</span> Fix documentation bugs associated with migration from optparse to argparse</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

273

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<td class="diff-line-num new_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">

260

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

<pre style="margin: 0;"> <span id="LC260" class="line" lang="markdown"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

274

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<td class="diff-line-num new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

261

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

<pre style="margin: 0;"> <span id="LC261" class="line" lang="markdown">v1.0 (2016.07.29)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

275

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<td class="diff-line-num new_line old" data-linenumber="262" style="width: 35px; color: rgba(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="LC275" class="line" lang="markdown"><span class="gh" style="color: #999;"><span class="idiff left right">-----------------</span></span></span>

</pre>

</td>

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

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

262

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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="LC262" class="line" lang="markdown"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

276

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<td class="diff-line-num new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

263

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="markdown"><span class="p">*</span> Initial release (forked from cutadapt 1.10)</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

277

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<td class="diff-line-num new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

264

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

<pre style="margin: 0;"> <span id="LC264" class="line" lang="markdown"><span class="p">*</span> Re-wrote much of filters.py and modifiers.py to separate modifying/filtering from file writing.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

278

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<td class="diff-line-num new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

265

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="markdown"><span class="p">    *</span> File writing is now managed by a separate class (seqio.Writers)</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">

<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#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">

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="make"><span class="nv" style="color: #008080;">tests</span> <span class="o" style="font-weight: 600;">=</span> tests</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="make"><span class="nv" style="color: #008080;">module</span> <span class="o" style="font-weight: 600;">=</span> atropos</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

3

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#pytestops = <span class="idiff left right">"--full-trace"</span></span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC4" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#pytestops = <span class="idiff left right">"-v -s"</span></span></span>

</pre>

</td>

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<td class="diff-line-num new old_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">

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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="make"><span class="c" style="color: #998; font-style: italic;">#pytestops = <span class="idiff left right">--full-trace</span></span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_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">

</td>

<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

</td>

<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="make"><span class="c" style="color: #998; font-style: italic;">#pytestops = <span class="idiff left right">-v -s</span></span></span>

</pre>

</td>

</tr>

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

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

5

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

5

</td>

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">repo</span> <span class="o" style="font-weight: 600;">=</span> jdidion/<span class="nv" style="color: #008080;">$(module)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

6

</td>

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

<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"><span class="nv" style="color: #008080;">desc</span> <span class="o" style="font-weight: 600;">=</span> Release <span class="nv" style="color: #008080;">$(version)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

</td>

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

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

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

8

</td>

<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">BUILD</span> <span class="o" style="font-weight: 600;">=</span><span class="idiff left"> python setup.py build_ext </span><span class="nt" style="color: #000080;"><span class="idiff">-i</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">&&</span></span><span class="idiff"> python setup.py </span><span class="nb" style="color: #0086b3;"><span class="idiff">install</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(installargs)</span></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="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

9

</td>

<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">TEST</span> <span class="o" style="font-weight: 600;">=</span><span class="idiff left"> py.test </span><span class="nv" style="color: #008080;"><span class="idiff">$(pytestops)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(tests)</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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

</td>

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="make"><span class="nv" style="color: #008080;">BUILD</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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

</td>

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="make"><span class="nv" style="color: #008080;">TEST</span> <span class="o" style="font-weight: 600;">=</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

10

</td>

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

<pre style="margin: 0;"> <span id="LC10" class="line" lang="make"></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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

11

</td>

<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC11" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

</td>

<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC12" class="line" lang="make">  <span class="nv" style="color: #008080;">$(BUILD)</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="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

<td class="diff-line-num new_line old" data-linenumber="11" style="width: 35px; color: rgba(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="LC13" class="line" lang="make">  <span class="nv" style="color: #008080;">$(TEST)</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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

</td>

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="make"><span class="nl">all</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean install test</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

</td>

<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

</td>

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

<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"></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="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC15" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

<td class="diff-line-num new_line old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC16" class="line" lang="make">  <span class="nv" style="color: #008080;">$(BUILD)</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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

13

</td>

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="make"><span class="nl">build</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="17" style="width: 35px; color: rgba(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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

14

</td>

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="make">  python setup.py build_ext <span class="nt" style="color: #000080;">-i</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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

15

</td>

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="make">  python setup.py sdist bdist_wheel</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="17" style="width: 35px; color: rgba(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="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

16

</td>

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

<pre style="margin: 0;">+<span id="LC16" class="line" lang="make"></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="17" style="width: 35px; color: rgba(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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

</td>

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="make"><span class="nl">install</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean build</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="17" style="width: 35px; color: rgba(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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

</td>

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="make">  python setup.py <span class="nb" style="color: #0086b3;">install</span> <span class="nv" style="color: #008080;">$(installargs)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

17

</td>

<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

19

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

18

</td>

<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

</td>

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

<pre style="margin: 0;"> <span id="LC20" class="line" lang="make"><span class="nl">test</span><span class="o" style="font-weight: 600;">:</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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

<td class="diff-line-num new_line old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

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

</pre>

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

</td>

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

21

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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="LC21" class="line" lang="make">  <span class="idiff left">py.test </span><span class="nv" style="color: #008080;"><span class="idiff">$(pytestops)</span></span><span class="idiff"> </span><span class="nv" style="color: #008080;"><span class="idiff right">$(tests</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

20

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<td class="diff-line-num new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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

<pre style="margin: 0;"> <span id="LC22" 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">

21

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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">

23

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

<pre style="margin: 0;"> <span id="LC23" 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="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

22

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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">

24

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

<pre style="margin: 0;"> <span id="LC24" 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 unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" style="width: 35px; color: rgba(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">@@ -48,21 +50,14 @@ docker:</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

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="make">  docker login <span class="nt" style="color: #000080;">-u</span> jdidion <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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<td class="diff-line-num 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">

51

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

<pre style="margin: 0;"> <span id="LC51" class="line" lang="make">  docker push <span class="nv" style="color: #008080;">$(repo)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

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<td class="diff-line-num new_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">

52

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

<pre style="margin: 0;"> <span id="LC52" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

51

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<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(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="LC51" class="line" lang="make"><span class="nl">release</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

52

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<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(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="LC52" class="line" lang="make">  <span class="nv" style="color: #008080;">$(clean)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

53

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<td class="diff-line-num new_line old" data-linenumber="53" style="width: 35px; color: rgba(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="LC53" class="line" lang="make">  <span class="c" style="color: #998; font-style: italic;"># tag</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="54" style="width: 35px; color: rgba(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="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

53

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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="LC53" class="line" lang="make"><span class="nl">tag</span><span class="o" style="font-weight: 600;">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

54

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC54" class="line" lang="make">  git tag <span class="nv" style="color: #008080;">$(version)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

55

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<td class="diff-line-num new_line old" data-linenumber="55" style="width: 35px; color: rgba(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="LC55" class="line" lang="make">  <span class="c" style="color: #998; font-style: italic;"># build</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

56

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<td class="diff-line-num new_line old" data-linenumber="55" style="width: 35px; color: rgba(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="LC56" class="line" lang="make">  <span class="nv" style="color: #008080;">$(BUILD)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

57

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<td class="diff-line-num new_line old" data-linenumber="55" style="width: 35px; color: rgba(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="LC57" class="line" lang="make">  <span class="nv" style="color: #008080;">$(TEST)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

58

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<td class="diff-line-num new_line old" data-linenumber="55" style="width: 35px; color: rgba(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="LC58" class="line" lang="make">  python setup.py sdist bdist_wheel</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

59

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<td class="diff-line-num new_line old" data-linenumber="55" style="width: 35px; color: rgba(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="LC59" class="line" lang="make">  <span class="c" style="color: #998; font-style: italic;"># release</span></span>

</pre>

</td>

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

60

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<td class="diff-line-num new_line old" data-linenumber="55" style="width: 35px; color: rgba(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="LC60" class="line" lang="make">  python setup.py sdist upload <span class="nt" style="color: #000080;">-r</span> pypi</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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="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">

55

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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="LC55" class="line" lang="make"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="make"><span class="nl">release</span><span class="o" style="font-weight: 600;">:</span> <span class="nf" style="color: #900; font-weight: 600;">clean tag install test</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(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="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

57

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="make">  twine upload dist/<span class="k" style="font-weight: 600;">*</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

61

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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">

58

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<pre style="margin: 0;"> <span id="LC58" 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 old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

62

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<td class="diff-line-num new_line old" data-linenumber="59" style="width: 35px; color: rgba(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="LC62" class="line" lang="make">  <span class="nv" style="color: #008080;">$(github_release)</span></span>

</pre>

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

63

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<td class="diff-line-num new_line old" data-linenumber="59" style="width: 35px; color: rgba(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="make">  <span class="nv" style="color: #008080;">$(docker)</span></span>

</pre>

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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="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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<pre style="margin: 0;"> <span id="LC59" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;">-<span id="LC65" class="line" lang="make"><span class="nl"><span class="idiff left">github_release</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">:</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="66" style="width: 35px; color: rgba(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="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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<pre style="margin: 0;">+<span id="LC60" class="line" lang="make"><span class="idiff left"> </span><span class="c" style="color: #998; font-style: italic;"><span class="idiff right"># github release</span></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">

66

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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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<pre style="margin: 0;"> <span id="LC61" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">curl</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-v</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-i</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-X</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">POST</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

67

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<td class="diff-line-num new_line" data-linenumber="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="nl">-H "Content-Type</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">application/json" </span>\</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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="nf" style="color: #900; font-weight: 600;">                -H "Authorization: token $(token)" </span>\</span>

</pre>

</td>

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<br>

</li>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,8 +26,7 @@ Atropos is available from [pypi](https://pypi.python.org/pypi/atropos) and can b</td>

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26

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

28

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="p">*</span> Required</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="markdown"><span class="p">    *</span> Python 3.3+ (python 2.x is NOT supported)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

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<td class="diff-line-num new_line old" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="markdown"><span class="p">        -</span> note: we have identified a possible bug in python 3.4.2 that causes random segmentation faults. We think this mainly affects unit testing (and thus specifically test on 3.4.3). If you encounter this bug, we recommend upgrading to a newer python version.</span>

</pre>

</td>

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

</td>

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

29

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

<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p">    *</span> Python 3.4.5+ (python 2.x is NOT supported)</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown"><span class="p">    *</span> Cython 0.25.2+ (<span class="sb" style="color: #d14;">`pip install Cython`</span>)</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

32

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"><span class="p">*</span> Maybe python libraries</span>

</pre>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="p">    *</span> pytest (for running unit tests)</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">@@ -197,6 +196,7 @@ The citation for the original Cutadapt paper is:</td>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="markdown"><span class="p">*</span> Scythe is an interesting new trimmer. Depending on how the benchmarks look in the forthcoming paper, we will add it to the list of tools we compare against Atropos, and perhaps implement their Bayesian approach for adapter match.</span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="markdown"><span class="p">*</span> Experiment with replacing the multicore implementation with an asyncio-based implementation (using ProcessPoolExecutor and uvloop).</span>

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<pre style="margin: 0;"> <span id="LC198" class="line" lang="markdown"><span class="p">*</span> Automatic adaptive tuning of queue sizes to maximize the balance between memory usage and latency.</span>

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<pre style="margin: 0;">+<span id="LC199" class="line" lang="markdown"><span class="p">*</span> FastProNGS has some nice visualizations that could be included, rather than relying on MultiQC: https://github.com/Megagenomics/FastProNGS</span>

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

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="markdown">While we consider the command-line interface to be stable, the internal code organization of Atropos is likely to change. At this time, we recommend to not directly interface with Atropos as a library (or to be prepared for your code to break). The internal code organization will be stabilized as of version 2.0, which is planned for sometime in 2017.</span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="markdown"></span>

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<br>

</li>

<li id="e14d2613b23186c0c8a0c4d5d16951517ef1d5af">

<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#e14d2613b23186c0c8a0c4d5d16951517ef1d5af"><strong>atropos/_version.py</strong></a>

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<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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<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>

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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>

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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>

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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;">" (<span class="idiff left right">tag: 1.1.22</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="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;">" (<span class="idiff left right">HEAD -> 1.1, tag: 1.1.24</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">9281be92f0e52a14085841344a509f7808efcfe1</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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<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#fbbf6d960c8a09ddcb61bf36ff75c30c2ae6fe6b"><strong>atropos/align/__init__.py</strong></a>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python">    <span class="s" style="color: #d14;">"seq_after"</span><span class="p">,</span> <span class="s" style="color: #d14;">"adapter_name"</span><span class="p">,</span> <span class="s" style="color: #d14;">"qual_before"</span><span class="p">,</span> <span class="s" style="color: #d14;">"qual_adapter"</span><span class="p">,</span> <span class="s" style="color: #d14;">"qual_after"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python">    <span class="s" style="color: #d14;">"is_front"</span><span class="p">,</span> <span class="s" style="color: #d14;">"asize"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rsize_adapter"</span><span class="p">,</span> <span class="s" style="color: #d14;">"rsize_total"</span><span class="p">))</span></span>

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

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Alternative semi-global alignment (</span></span>

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># http://www.bioinf.uni-freiburg.de/Lehre/Courses/2013_SS/V_Bioinformatik_1/lecture4.pdf)</span></span>

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># strategies designed to improve insert matching of paired-end reads.</span></span>

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Note: these are currently just prototype implementations. They will need to be optimized</span></span>

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># using numpy and/or re-written in cython.</span></span>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 1. SeqPurge algorithm: insert match algorithm that performs thresholded exhaustive</span></span>

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    comparison to minimize probability of incorrect alignment. Relies on the fact that</span></span>

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<pre style="margin: 0;">-<span id="LC186" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    overlapping reads share alleles and indels (i.e. no gaps are required) (in C++).</span></span>

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    https://github.com/imgag/ngs-bits/tree/master/src/SeqPurge.</span></span>

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#   * Speed up sequence comparison:</span></span>

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<pre style="margin: 0;">-<span id="LC189" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     * Between adapters and overhangs:</span></span>

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#       * http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4080745/pdf/btu177.pdf</span></span>

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#     * Between reads:</span></span>

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192

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#       * http://bioinformatics.oxfordjournals.org/content/30/14/2000.abstract</span></span>

</pre>

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193

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 2. Skewer algorithm: bit-masked k-difference matching (in C++).</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

194

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    https://github.com/relipmoc/skewer</span></span>

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<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

195

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 3. Quality-aware overlap alignment (in Haskell).</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

196

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    https://hackage.haskell.org/package/bio-0.5.3/docs/Bio-Alignment-QAlign.html</span></span>

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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

197

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<pre style="margin: 0;">-<span id="LC197" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 4. FOGSAA, modified for semi-global alignment.</span></span>

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<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

198

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    http://www.nature.com/articles/srep01746</span></span>

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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

199

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    http://www.isical.ac.in/~bioinfo_miu/FOGSAA.7z</span></span>

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200

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 5. EDLIB: edit distance-based alignment</span></span>

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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

201

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#    https://github.com/Martinsos/edlib</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="202" style="width: 35px; color: rgba(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="LC202" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 6. Phred-adjusted ML for error probability:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

203

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># https://biosails.github.io/pheniqs/glossary.html#phred_adjusted_maximum_likelihood_decoding</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

204

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 7. Adaptive banded alignment: https://github.com/ocxtal/libgaba</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

205

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># Also think about different sequence encodings that might enable faster alignment</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(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="LC206" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># https://github.com/hammerlab/kerseq/blob/master/kerseq/sequence_encoding.py</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="LC207" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 8. https://github.com/yamada-kd/nepal</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(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="LC208" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 9. The SeqAn C++ library implements several alignment algorithms:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

209

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># http://www.sciencedirect.com/science/article/pii/S0168165617315420</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(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="LC210" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 10. Could we treat paired end read + adapter alignment as an MSA problem?</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># 11. Look at alignment-free tools for pairwise sequence comparison:</span></span>

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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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<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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<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>

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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="LC177" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC178" 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="LC179" class="line" lang="python">    <span class="s" style="color: #d14;">"""Implementation of an insert matching algorithm.</span></span>

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<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#e8f677b53615a7ffaf54ba5416957562ba27e685"><strong>atropos/commands/legacy_report.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">@@ -15,7 +15,7 @@ INDENTED = textwrap.TextWrapper(initial_indent=INDENT, subsequent_indent=INDENT)</td>

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Printer</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="LC17" class="line" lang="python">    <span class="s" style="color: #d14;">"""Manages printing to a file.</span></span>

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

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: The output file.</span></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="python"><span class="s" style="color: #d14;">        kwargs: Additional keyword arguments passed to the print function.</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,7 +24,7 @@ class Printer(object):</td>

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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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<pre style="margin: 0;"> <span id="LC24" 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;">outfile</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">outfile</span></span>

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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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<pre style="margin: 0;"> <span id="LC25" 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;">indent</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">indent</span></span>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">print_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span></span>

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<td class="diff-line-num new_line old" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" 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="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC28" 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 class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="n" style="color: #333;">indent</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</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="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">indent</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 old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">            <span class="n" style="color: #333;">indent</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;">indent</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">indent</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,7 +33,7 @@ class Printer(object):</td>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">indent</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC34" 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;">_print</span><span class="p">(</span><span class="n" style="color: #333;">indent</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">''</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC35" 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;">_print</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="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 new_line old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" 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="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_print</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;">args</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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<pre style="margin: 0;"> <span id="LC38" 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;">print_args</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python">            <span class="n" style="color: #333;">print_args</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;">print_args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">()</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,7 +41,7 @@ class Printer(object):</td>

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

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

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<pre style="margin: 0;"> <span id="LC41" 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="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">            <span class="n" style="color: #333;">print_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">kwargs</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</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;">outfile</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">print_args</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

44

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<td class="diff-line-num new_line old" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC44" 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="45" style="width: 35px; color: rgba(0,0,0,0.3); 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="44" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC44" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); 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="45" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC45" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">newline</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="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="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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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">        <span class="s" style="color: #d14;">"""Print a newline.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<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">

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<pre style="margin: 0;"> <span id="LC47" 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="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,7 +49,7 @@ class Printer(object):</td>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); 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="50" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC50" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">TitlePrinter</span><span class="p">(</span><span class="n" style="color: #333;">Printer</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num 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">

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(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="52" style="width: 35px; color: rgba(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="LC52" 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 old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: The output file.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;">        levels: The formatting associated with different header levels.</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -61,10 +61,10 @@ class TitlePrinter(Printer):</td>

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<pre style="margin: 0;"> <span id="LC61" 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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<pre style="margin: 0;"> <span id="LC62" 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;">outfile</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="LC63" 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;">levels</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">levels</span></span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC65" 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 class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">level</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;">newline</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</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="LC66" class="line" lang="python">        <span class="n" style="color: #333;">title</span> <span class="o" style="font-weight: 600;">=</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 class="n" style="color: #333;">title</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">level</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="LC69" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">level</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;">levels</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC70" 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 level: {}"</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;">level</span><span class="p">))</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" style="width: 35px; color: rgba(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="74" style="width: 35px; color: rgba(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">@@ -74,18 +74,18 @@ class TitlePrinter(Printer):</td>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python">            <span class="n" style="color: #333;">width</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;">title</span><span class="p">)</span></span>

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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;">overline</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC76" 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;">_print</span><span class="p">(</span><span class="n" style="color: #333;">overline</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">width</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="LC77" class="line" lang="python"><span class="idiff left right">        </span></span>

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

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<pre style="margin: 0;"> <span id="LC78" 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;">_print</span><span class="p">(</span><span class="n" style="color: #333;">title</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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<pre style="margin: 0;">-<span id="LC79" class="line" lang="python"><span class="idiff left right">        </span></span>

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

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">level</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="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">underline</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC81" 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;">_print</span><span class="p">(</span><span class="n" style="color: #333;">underline</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">width</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="LC82" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">newline</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC84" 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;">newline</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RowPrinter</span><span class="p">(</span><span class="n" style="color: #333;">Printer</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">    <span class="s" style="color: #d14;">"""Priter that formats rows in a table.</span></span>

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<pre style="margin: 0;">-<span id="LC88" 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="LC88" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: The output file.</span></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="python"><span class="s" style="color: #d14;">        colwidths: Column widths.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="94" style="width: 35px; color: rgba(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">@@ -94,7 +94,7 @@ class RowPrinter(Printer):</td>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python"><span class="s" style="color: #d14;">        pct: Whether floats should be formatted as percentages.</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"><span class="s" style="color: #d14;">        default: Default value for None's.</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"><span class="s" style="color: #d14;">        kwargs: Additional keyword arguments passed to the print function.</span></span>

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<pre style="margin: 0;">-<span id="LC97" 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="LC97" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python"><span class="s" style="color: #d14;">    colwidths, justification, and indent can be longer or shorter than the</span></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python"><span class="s" style="color: #d14;">    number of arguments; if shorter, the last value in the list is repeated;</span></span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"><span class="s" style="color: #d14;">    if longer, the list is truncated.</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">@@ -110,10 +110,10 @@ class RowPrinter(Printer):</td>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python">                <span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">)))</span></span>

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<pre style="margin: 0;"> <span id="LC111" 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;">pct</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pct</span></span>

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<pre style="margin: 0;"> <span id="LC112" 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;">default</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">default</span></span>

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<pre style="margin: 0;">-<span id="LC113" 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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_rows</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;">rows</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</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="LC115" class="line" lang="python">        <span class="s" style="color: #d14;">"""Print multiple rows. Automatically figures out column widths.</span></span>

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<pre style="margin: 0;">-<span id="LC116" 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="LC116" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;">        Args:</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;">            rows: Rows to print.</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;">            header: Header row.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="126" style="width: 35px; color: rgba(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">@@ -126,7 +126,7 @@ class RowPrinter(Printer):</td>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python">                <span class="n" style="color: #333;">header_rows</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">header</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC127" 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="LC128" class="line" lang="python">                <span class="n" style="color: #333;">header_widths</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">header_part</span><span class="p">)</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python">                    <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">sizeof</span><span class="p">(</span><span class="n" style="color: #333;">h</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">h</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">header_part</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">header_part</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">header</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">                <span class="n" style="color: #333;">header_rows</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;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">header</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python">            <span class="n" style="color: #333;">colwidths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -136,13 +136,13 @@ class RowPrinter(Printer):</td>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python">                <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;">header_row</span><span class="p">,</span> <span class="n" style="color: #333;">colwidths</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">colwidths</span><span class="p">,</span> <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">i</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;">header_rows</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="LC137" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">row</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">rows</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python">            <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;">row</span><span class="p">,</span> <span class="n" style="color: #333;">colwidths</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">colwidths</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="python"><span class="idiff left right">    </span></span>

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

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<pre style="margin: 0;"> <span id="LC140" 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>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">            <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;">args</span><span class="p">,</span> <span class="n" style="color: #333;">colwidths</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;">extra_width</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;">justification</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="LC142" class="line" lang="python">            <span class="n" style="color: #333;">extra_justification</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;">indent</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;">extra_indent</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="LC143" class="line" lang="python">            <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span> <span class="n" style="color: #333;">underline</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'-'</span><span class="p">,</span> <span class="n" style="color: #333;">pct</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</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="LC144" class="line" lang="python">        <span class="s" style="color: #d14;">"""Print a row.</span></span>

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<pre style="margin: 0;">-<span id="LC145" 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="LC145" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;">        Args:</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="python"><span class="s" style="color: #d14;">            args: Fields in the row.</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="python"><span class="s" style="color: #d14;">            colwidths, justification, indent: Row-specific colwidths,</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">@@ -161,10 +161,10 @@ class RowPrinter(Printer):</td>

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<pre style="margin: 0;"> <span id="LC161" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">ncols</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="LC162" 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;">newline</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span></span>

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pct</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="LC166" class="line" lang="python">            <span class="n" style="color: #333;">pct</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;">pct</span></span>

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC167" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">adjust</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">extra</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="LC169" class="line" lang="python">            <span class="s" style="color: #d14;">"""Adjust an array. If longer than the number of columns,</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python"><span class="s" style="color: #d14;">            truncate; if shorter, fill in by repeating the last element.</span></span>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -176,7 +176,7 @@ class RowPrinter(Printer):</td>

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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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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">arr</span><span class="p">[:</span><span class="n" style="color: #333;">ncols</span><span class="p">]</span></span>

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<td class="diff-line-num old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC177" 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="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">

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python">                <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">arr</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="n" style="color: #333;">extra</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">arr</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 class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">ncols</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">alen</span><span class="p">))</span></span>

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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(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="179" style="width: 35px; color: rgba(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="LC179" 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="180" style="width: 35px; color: rgba(0,0,0,0.3); 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="179" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC179" class="line" lang="python"></span>

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<td class="diff-line-num old_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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<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="python">        <span class="n" style="color: #333;">colwidths</span><span class="p">,</span> <span class="n" style="color: #333;">justification</span><span class="p">,</span> <span class="n" style="color: #333;">indent</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="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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<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="python">            <span class="n" style="color: #333;">adjust</span><span class="p">(</span><span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">extra</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); 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="182" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC182" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">arr</span><span class="p">,</span> <span class="n" style="color: #333;">extra</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" style="width: 35px; color: rgba(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="185" style="width: 35px; color: rgba(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">@@ -185,13 +185,13 @@ class RowPrinter(Printer):</td>

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<td class="diff-line-num old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC185" class="line" lang="python">                    <span class="n" style="color: #333;">justification</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;">justification</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC186" class="line" lang="python">                    <span class="n" style="color: #333;">indent</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;">indent</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); 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="187" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC187" class="line" lang="python">                <span class="p">(</span><span class="n" style="color: #333;">extra_width</span><span class="p">,</span> <span class="n" style="color: #333;">extra_justification</span><span class="p">,</span> <span class="n" style="color: #333;">extra_indent</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(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="188" style="width: 35px; color: rgba(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="LC188" 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="189" style="width: 35px; color: rgba(0,0,0,0.3); 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="188" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC188" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); 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="189" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC189" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># adjust colwidths if this is a header</span></span>

</pre>

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

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

190

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="191" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC191" class="line" lang="python">            <span class="n" style="color: #333;">colwidths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">                <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">w</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="p">)))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">w</span><span class="p">,</span> <span class="n" style="color: #333;">a</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">colwidths</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC194" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python">        <span class="n" style="color: #333;">fmt_str</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">        <span class="n" style="color: #333;">fmt_args</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">,</span> <span class="n" style="color: #333;">width</span><span class="p">,</span> <span class="n" style="color: #333;">just</span><span class="p">,</span> <span class="n" style="color: #333;">ind</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</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">@@ -210,10 +210,10 @@ class RowPrinter(Printer):</td>

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="python">                <span class="n" style="color: #333;">ind</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'{'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">':'</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">just</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">width</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;">ind</span><span class="p">))</span> <span class="o" style="font-weight: 600;">+</span></span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python">                <span class="n" style="color: #333;">typ</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'}'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python">            <span class="n" style="color: #333;">fmt_args</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;">value</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="python"><span class="idiff left right">        </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="n" style="color: #333;">fmt_str</span> <span class="o" style="font-weight: 600;">=</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 class="n" style="color: #333;">fmt_str</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC215" 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;">_print</span><span class="p">(</span><span class="n" style="color: #333;">fmt_str</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">fmt_args</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="LC216" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC216" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">header</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python">            <span class="n" style="color: #333;">sepline</span> <span class="o" style="font-weight: 600;">=</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 class="n" style="color: #333;">underline</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">width</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">width</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">colwidths</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC219" 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;">_print</span><span class="p">(</span><span class="n" style="color: #333;">sepline</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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -228,12 +228,12 @@ class LegacyReportGenerator(BaseReportGenerator):</td>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">generate_report</span><span class="p">(</span><span class="n" style="color: #333;">summary</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="python">    <span class="s" style="color: #d14;">"""Generate a report.</span></span>

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

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"><span class="s" style="color: #d14;">        summary: The summary dict.</span></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: The output file name/object.</span></span>

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

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<pre style="margin: 0;">-<span id="LC236" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python">    <span class="n" style="color: #333;">print_summary_report</span><span class="p">(</span><span class="n" style="color: #333;">summary</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'trim'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">summary</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">        <span class="n" style="color: #333;">print_trim_report</span><span class="p">(</span><span class="n" style="color: #333;">summary</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_summary_report</span><span class="p">(</span><span class="n" style="color: #333;">summary</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python">    <span class="s" style="color: #d14;">"""Print the top-level summary report.</span></span>

</pre>

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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>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="247" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC247" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="248" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC248" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="249" style="width: 35px; color: rgba(0,0,0,0.3); 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="249" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC249" class="line" lang="python"><span class="s" style="color: #d14;">        summary: The summary dict.</span></span>

</pre>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: The output file object.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="251" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC251" 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="252" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC252" class="line" lang="python">    <span class="n" style="color: #333;">_print_title</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TitlePrinter</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="253" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC253" class="line" lang="python">    <span class="n" style="color: #333;">_print</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Printer</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC254" 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="255" style="width: 35px; color: rgba(0,0,0,0.3); 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="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>

</pre>

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<td class="diff-line-num old_line" data-linenumber="255" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC255" class="line" lang="python">    <span class="n" style="color: #333;">_print_title</span><span class="p">(</span><span class="s" style="color: #d14;">"Atropos"</span><span class="p">,</span> <span class="n" style="color: #333;">level</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="256" style="width: 35px; color: rgba(0,0,0,0.3); 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="256" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC256" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Atropos version: {}"</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;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'version'</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); 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="257" style="width: 35px; color: rgba(0,0,0,0.3); 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="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Python version: {}"</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;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'python'</span><span class="p">]))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); 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="258" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC258" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Command line parameters: {} {}"</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="259" style="width: 35px; color: rgba(0,0,0,0.3); 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="259" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC259" class="line" lang="python">        <span class="n" style="color: #333;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'command'</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 class="n" style="color: #333;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'options'</span><span class="p">][</span><span class="s" style="color: #d14;">'orig_args'</span><span class="p">])))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC261" 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="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Sample ID: {}"</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;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'sample_id'</span><span class="p">]))</span></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Input format: {}"</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;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'derived'</span><span class="p">][</span><span class="s" style="color: #d14;">'input_format'</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;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Input files:"</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="266" style="width: 35px; color: rgba(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="266" style="width: 35px; color: rgba(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">@@ -266,7 +266,7 @@ def print_summary_report(summary, outfile):</td>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">infile</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="LC267" class="line" lang="python">            <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="n" style="color: #333;">infile</span><span class="p">,</span> <span class="n" style="color: #333;">indent</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">INDENT</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python">    <span class="n" style="color: #333;">timing</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;">'timing'</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python">    <span class="n" style="color: #333;">total</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;">"total_record_count"</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;">wctime</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Wallclock time: {:.2F} s"</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;">timing</span><span class="p">[</span><span class="s" style="color: #d14;">"wallclock"</span><span class="p">])]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="281" style="width: 35px; color: rgba(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="281" style="width: 35px; color: rgba(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">@@ -281,7 +281,7 @@ def print_summary_report(summary, outfile):</td>

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<pre style="margin: 0;"> <span id="LC281" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC282" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_trim_report</span><span class="p">(</span><span class="n" style="color: #333;">summary</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC283" class="line" lang="python">    <span class="s" style="color: #d14;">"""Print the trimming report.</span></span>

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<pre style="margin: 0;">-<span id="LC284" 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="LC284" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"><span class="s" style="color: #d14;">        summary: Summary dict.</span></span>

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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: Open output stream.</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">@@ -292,17 +292,18 @@ def print_trim_report(summary, outfile):</td>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python">    <span class="n" style="color: #333;">max_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">total_bp</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC293" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># account for commas</span></span>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="python">    <span class="n" style="color: #333;">max_width</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">max_width</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">3</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="python"><span class="idiff left right">    </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="n" style="color: #333;">_print_title</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TitlePrinter</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC297" class="line" lang="python">    <span class="n" style="color: #333;">_print</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RowPrinter</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">35</span><span class="p">,</span> <span class="n" style="color: #333;">max_width</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python">    <span class="n" style="color: #333;">total</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;">"total_record_count"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC300" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">total</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="LC301" class="line" lang="python">        <span class="n" style="color: #333;">_print</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python">        <span class="n" style="color: #333;">_print_error</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Printer</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="python">        <span class="n" style="color: #333;">_print_error</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python">            <span class="s" style="color: #d14;">"No reads processed! Either your input file is empty or you "</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python">            <span class="s" style="color: #d14;">"used the wrong -f/--format parameter."</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span></span>

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<pre style="margin: 0;">-<span id="LC305" 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="306" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC306" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="306" style="width: 35px; color: rgba(0,0,0,0.3); 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="307" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC307" class="line" lang="python">    <span class="n" style="color: #333;">modifiers</span><span class="p">,</span> <span class="n" style="color: #333;">filters</span><span class="p">,</span> <span class="n" style="color: #333;">formatters</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span></span>

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<td class="diff-line-num old_line" data-linenumber="307" style="width: 35px; color: rgba(0,0,0,0.3); 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="308" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC308" class="line" lang="python">        <span class="n" style="color: #333;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'trim'</span><span class="p">][</span><span class="n" style="color: #333;">key</span><span class="p">]</span></span>

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<td class="diff-line-num new_line" data-linenumber="309" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC309" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'modifiers'</span><span class="p">,</span> <span class="s" style="color: #d14;">'filters'</span><span class="p">,</span> <span class="s" style="color: #d14;">'formatters'</span><span class="p">))</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="322" style="width: 35px; color: rgba(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="323" style="width: 35px; color: rgba(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">@@ -322,7 +323,7 @@ def print_trim_report(summary, outfile):</td>

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<pre style="margin: 0;"> <span id="LC323" class="line" lang="python">            <span class="n" style="color: #333;">trimmers</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;">name</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">correction_enabled</span> <span class="ow" style="font-weight: 600;">and</span> <span class="s" style="color: #d14;">'records_corrected'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mod</span><span class="p">:</span></span>

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<td class="diff-line-num new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC325" class="line" lang="python">            <span class="n" style="color: #333;">corrected</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mod</span></span>

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<pre style="margin: 0;">-<span id="LC325" 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="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC326" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC327" class="line" lang="python">    <span class="n" style="color: #333;">_print_title</span><span class="p">(</span><span class="s" style="color: #d14;">"Trimming"</span><span class="p">,</span> <span class="n" style="color: #333;">level</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 new_line" data-linenumber="328" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC328" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="n" style="color: #333;">pairs_or_reads</span><span class="p">,</span> <span class="s" style="color: #d14;">'records'</span><span class="p">,</span> <span class="s" style="color: #d14;">'fraction'</span><span class="p">,</span> <span class="n" style="color: #333;">header</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 new_line" data-linenumber="329" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC329" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span></span>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="343" style="width: 35px; color: rgba(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">@@ -342,38 +343,38 @@ def print_trim_report(summary, outfile):</td>

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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="343" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC343" class="line" lang="python">                <span class="n" style="color: #333;">adapter_cutter</span><span class="p">[</span><span class="s" style="color: #d14;">'records_with_adapters'</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="343" style="width: 35px; color: rgba(0,0,0,0.3); 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="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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<pre style="margin: 0;"> <span id="LC344" class="line" lang="python">                <span class="n" style="color: #333;">adapter_cutter</span><span class="p">[</span><span class="s" style="color: #d14;">'fraction_records_with_adapters'</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="345" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC345" class="line" lang="python">                <span class="n" style="color: #333;">pct</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 new_line old" data-linenumber="346" style="width: 35px; color: rgba(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>

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<pre style="margin: 0;">+<span id="LC346" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_print_filter</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">filters</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python">            <span class="n" style="color: #333;">_print</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC350" class="line" lang="python">                <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 class="n" style="color: #333;">pairs_or_reads</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">replace</span><span class="p">(</span><span class="s" style="color: #d14;">'_'</span><span class="p">,</span> <span class="s" style="color: #d14;">' '</span><span class="p">)),</span></span>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python">                <span class="n" style="color: #333;">filters</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">][</span><span class="s" style="color: #d14;">'records_filtered'</span><span class="p">],</span></span>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python">                <span class="n" style="color: #333;">filters</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">][</span><span class="s" style="color: #d14;">'fraction_records_filtered'</span><span class="p">],</span> <span class="n" style="color: #333;">pct</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="LC352" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC353" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC354" class="line" lang="python">    <span class="n" style="color: #333;">_print_filter</span><span class="p">(</span><span class="s" style="color: #d14;">'too_short'</span><span class="p">,</span> <span class="s" style="color: #d14;">'that were'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python">    <span class="n" style="color: #333;">_print_filter</span><span class="p">(</span><span class="s" style="color: #d14;">'too_long'</span><span class="p">,</span> <span class="s" style="color: #d14;">'that were'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python">    <span class="n" style="color: #333;">_print_filter</span><span class="p">(</span><span class="s" style="color: #d14;">'too_many_n'</span><span class="p">,</span> <span class="s" style="color: #d14;">'with'</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC356" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span></span>

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<td class="diff-line-num new_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC359" class="line" lang="python">        <span class="s" style="color: #d14;">"{} written (passing filters):"</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;">pairs_or_reads</span><span class="p">),</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC360" class="line" lang="python">        <span class="n" style="color: #333;">formatters</span><span class="p">[</span><span class="s" style="color: #d14;">'records_written'</span><span class="p">],</span> <span class="n" style="color: #333;">formatters</span><span class="p">[</span><span class="s" style="color: #d14;">'fraction_records_written'</span><span class="p">],</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python">        <span class="n" style="color: #333;">pct</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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<pre style="margin: 0;">-<span id="LC361" 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="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); 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="363" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC363" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">corrected</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="n" style="color: #333;">_print</span><span class="p">(</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="python">            <span class="s" style="color: #d14;">"Pairs corrected:"</span><span class="p">,</span> <span class="n" style="color: #333;">corrected</span><span class="p">[</span><span class="s" style="color: #d14;">'records_corrected'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num 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">

365

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<td class="diff-line-num new_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC366" class="line" lang="python">            <span class="n" style="color: #333;">corrected</span><span class="p">[</span><span class="s" style="color: #d14;">'fraction_records_corrected'</span><span class="p">],</span> <span class="n" style="color: #333;">pct</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 new_line old" data-linenumber="367" style="width: 35px; color: rgba(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="LC366" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); 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="368" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC368" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="LC369" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Base pairs"</span><span class="p">,</span> <span class="s" style="color: #d14;">'bp'</span><span class="p">,</span> <span class="s" style="color: #d14;">'fraction'</span><span class="p">,</span> <span class="n" style="color: #333;">header</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 new_line old" data-linenumber="370" style="width: 35px; color: rgba(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="LC369" 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="370" style="width: 35px; color: rgba(0,0,0,0.3); 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="370" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC370" class="line" lang="python"></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">

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC371" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Total bp processed:"</span><span class="p">,</span> <span class="n" style="color: #333;">total_bp</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_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">

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

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

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC373" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">2</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">

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<td class="diff-line-num new_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC374" class="line" lang="python">            <span class="n" style="color: #333;">_print</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="374" style="width: 35px; color: rgba(0,0,0,0.3); 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="375" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC375" class="line" lang="python">                <span class="s" style="color: #d14;">"Read {}:"</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;">read</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">),</span> <span class="n" style="color: #333;">summary</span><span class="p">[</span><span class="s" style="color: #d14;">'total_bp_counts'</span><span class="p">][</span><span class="n" style="color: #333;">read</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); 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="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="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC376" class="line" lang="python">                <span class="n" style="color: #333;">indent</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">INDENT</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="376" style="width: 35px; color: rgba(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="377" style="width: 35px; color: rgba(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="LC376" 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="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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

<pre style="margin: 0;">+<span id="LC377" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_print_bp</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">default</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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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">paired</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="python">            <span class="n" style="color: #333;">_print</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">@@ -389,15 +390,15 @@ def print_trim_report(summary, outfile):</td>

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="python">            <span class="n" style="color: #333;">_print</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="python">                <span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'fraction_{}'</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;">key</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="392" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC392" class="line" lang="python">                <span class="n" style="color: #333;">pct</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">default</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="393" style="width: 35px; color: rgba(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="LC392" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC393" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC394" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">mod</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">trimmers</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); 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="395" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC395" class="line" lang="python">        <span class="n" style="color: #333;">_print_bp</span><span class="p">(</span><span class="n" style="color: #333;">mod</span><span class="p">[</span><span class="s" style="color: #d14;">'desc'</span><span class="p">],</span> <span class="n" style="color: #333;">mod</span><span class="p">,</span> <span class="s" style="color: #d14;">'bp_trimmed'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="396" style="width: 35px; color: rgba(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="LC395" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC396" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); 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="397" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC397" class="line" lang="python">    <span class="n" style="color: #333;">_print_bp</span><span class="p">(</span><span class="s" style="color: #d14;">"Total bp written (filtered):"</span><span class="p">,</span> <span class="n" style="color: #333;">formatters</span><span class="p">,</span> <span class="s" style="color: #d14;">'bp_written'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="398" style="width: 35px; color: rgba(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="LC397" 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="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC398" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC399" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">error_corrector</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); 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="400" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC400" class="line" lang="python">        <span class="n" style="color: #333;">_print_bp</span><span class="p">(</span><span class="s" style="color: #d14;">"Total bp corrected:"</span><span class="p">,</span> <span class="n" style="color: #333;">error_corrector</span><span class="p">,</span> <span class="s" style="color: #d14;">'bp_corrected'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="401" style="width: 35px; color: rgba(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="LC400" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC401" class="line" lang="python"></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;">adapter_cutter</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC403" class="line" lang="python">        <span class="n" style="color: #333;">_print</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC404" class="line" lang="python">        <span class="n" style="color: #333;">adapters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter_cutter</span><span class="p">[</span><span class="s" style="color: #d14;">'adapters'</span><span class="p">]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="405" style="width: 35px; color: rgba(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="406" style="width: 35px; color: rgba(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">@@ -405,12 +406,12 @@ def print_trim_report(summary, outfile):</td>

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

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<pre style="margin: 0;"> <span id="LC407" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_adapter_report</span><span class="p">(</span><span class="n" style="color: #333;">adapters</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">paired</span><span class="p">,</span> <span class="n" style="color: #333;">total_records</span><span class="p">,</span> <span class="n" style="color: #333;">max_width</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC408" class="line" lang="python">    <span class="s" style="color: #d14;">"""Print details for a adapters.</span></span>

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<pre style="margin: 0;">-<span id="LC408" 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="LC409" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"><span class="s" style="color: #d14;">        adapters: Sequence of adapter info dicts.</span></span>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: The output file</span></span>

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

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<pre style="margin: 0;"> <span id="LC413" class="line" lang="python"><span class="s" style="color: #d14;">        paired: Whether the data is paired-end.</span></span>

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<pre style="margin: 0;">-<span id="LC413" 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="LC414" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"><span class="s" style="color: #d14;">        max_width: Max column width.</span></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC417" class="line" lang="python">    <span class="n" style="color: #333;">adapter_lenghts</span> <span class="o" style="font-weight: 600;">=</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">@@ -424,15 +425,15 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python">                    <span class="n" style="color: #333;">adapter_lenghts</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">'sequence'</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python">    <span class="n" style="color: #333;">max_seq_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">adapter_lenghts</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC427" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC428" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC429" class="line" lang="python">    <span class="n" style="color: #333;">_print</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Printer</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python">    <span class="n" style="color: #333;">_print_title</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TitlePrinter</span><span class="p">(</span><span class="n" style="color: #333;">outfile</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;">_print_adj</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RowPrinter</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">),</span> <span class="n" style="color: #333;">pct</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">indent</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="n" style="color: #333;">INDENT</span><span class="p">,</span> <span class="s" style="color: #d14;">''</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC431" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC432" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC433" class="line" lang="python">    <span class="n" style="color: #333;">seq_printer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RowPrinter</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python">        <span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="p">(</span><span class="n" style="color: #333;">max_seq_len</span><span class="p">,</span> <span class="mi" style="color: #099;">14</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="n" style="color: #333;">max_width</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">'<'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<'</span><span class="p">,</span> <span class="s" style="color: #d14;">'>'</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python">    <span class="n" style="color: #333;">hist_printer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RowPrinter</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="n" style="color: #333;">justification</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">'>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'>'</span><span class="p">,</span> <span class="s" style="color: #d14;">'<'</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC435" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC437" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_error_ranges</span><span class="p">(</span><span class="n" style="color: #333;">adapter_length</span><span class="p">,</span> <span class="n" style="color: #333;">error_rate</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python">        <span class="s" style="color: #d14;">"""Print max number of errors for ranges of adapter match lengths.</span></span>

</pre>

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439

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -451,14 +452,14 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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<pre style="margin: 0;"> <span id="LC452" class="line" lang="python">            <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"{0}-{1} bp: {2}"</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="LC453" class="line" lang="python">                <span class="n" style="color: #333;">prev</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_length</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">adapter_length</span><span class="p">)))</span></span>

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<pre style="margin: 0;"> <span id="LC454" class="line" lang="python">        <span class="n" style="color: #333;">_print</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC454" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC455" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC456" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_histogram</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC456" class="line" lang="python">            <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_length</span><span class="p">,</span> <span class="n" style="color: #333;">num_reads</span><span class="p">,</span> <span class="n" style="color: #333;">error_rate</span><span class="p">,</span> <span class="n" style="color: #333;">errors</span><span class="p">,</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC457" class="line" lang="python">            <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_length</span><span class="p">,</span> <span class="n" style="color: #333;">num_reads</span><span class="p">,</span> <span class="n" style="color: #333;">error_rate</span><span class="p">,</span> <span class="n" style="color: #333;">errors</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC458" class="line" lang="python">            <span class="n" style="color: #333;">match_probabilities</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC459" class="line" lang="python">        <span class="s" style="color: #d14;">"""Print a histogram. Also, print the no. of reads expected to be</span></span>

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<pre style="margin: 0;"> <span id="LC460" class="line" lang="python"><span class="s" style="color: #d14;">        trimmed by chance (assuming a uniform distribution of nucleotides in</span></span>

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<pre style="margin: 0;"> <span id="LC461" class="line" lang="python"><span class="s" style="color: #d14;">        the reads).</span></span>

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<pre style="margin: 0;">-<span id="LC461" 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="LC462" class="line" lang="python"></span>

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

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<pre style="margin: 0;"> <span id="LC464" class="line" lang="python"><span class="s" style="color: #d14;">            data: A dictionary mapping lengths of trimmed sequences to their</span></span>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="python"><span class="s" style="color: #d14;">                respective frequency</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">@@ -480,9 +481,9 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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<pre style="margin: 0;"> <span id="LC481" class="line" lang="python">                <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="n" style="color: #333;">estimated</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python">                <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">error_rate</span> <span class="o" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">adapter_length</span><span class="p">))])</span></span>

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python">            <span class="n" style="color: #333;">hist_errors</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;">errors</span><span class="p">[</span><span class="s" style="color: #d14;">'rows'</span><span class="p">][</span><span class="n" style="color: #333;">length</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC483" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC484" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC485" class="line" lang="python">        <span class="n" style="color: #333;">col_sizes</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">col</span><span class="p">)))</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">col</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hist_errors</span><span class="p">)]</span></span>

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<pre style="margin: 0;">-<span id="LC485" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC486" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python">        <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_format_hist_errors</span><span class="p">(</span><span class="n" style="color: #333;">errs</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC488" class="line" lang="python">            <span class="n" style="color: #333;">trailing</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="LC489" class="line" lang="python">            <span class="n" style="color: #333;">hist_str</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="493" style="width: 35px; color: rgba(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="494" style="width: 35px; color: rgba(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">@@ -493,26 +494,26 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="python">                    <span class="n" style="color: #333;">trailing</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="python">                    <span class="n" style="color: #333;">hist_str</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">((</span><span class="s" style="color: #d14;">'{:<'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">col_sizes</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'d}'</span><span class="p">)</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;">e</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC496" 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="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">reversed</span><span class="p">(</span><span class="n" style="color: #333;">hist_str</span><span class="p">))</span></span>

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<pre style="margin: 0;">-<span id="LC496" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC497" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">errs</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">hist_errors</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC499" class="line" lang="python">            <span class="n" style="color: #333;">hist</span><span class="p">[</span><span class="n" style="color: #333;">i</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;">_format_hist_errors</span><span class="p">(</span><span class="n" style="color: #333;">errs</span><span class="p">))</span></span>

</pre>

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499

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<pre style="margin: 0;">-<span id="LC499" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

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500

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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="LC500" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="500" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

500

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501

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<pre style="margin: 0;"> <span id="LC501" class="line" lang="python">        <span class="n" style="color: #333;">error_header</span> <span class="o" style="font-weight: 600;">=</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>

</pre>

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501

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502

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python">            <span class="p">(</span><span class="s" style="color: #d14;">'{:<'</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'d}'</span><span class="p">)</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;">i</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="503" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC503" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">e</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">enumerate</span><span class="p">(</span><span class="n" style="color: #333;">col_sizes</span><span class="p">))</span></span>

</pre>

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503

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

</pre>

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<pre style="margin: 0;">+<span id="LC504" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

505

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="python">        <span class="n" style="color: #333;">hist_printer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">print_rows</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

505

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<td class="diff-line-num new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python">            <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">hist</span><span class="p">,</span></span>

</pre>

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506

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<td class="diff-line-num new_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

507

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<pre style="margin: 0;"> <span id="LC507" class="line" lang="python">            <span class="n" style="color: #333;">header</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span></span>

</pre>

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507

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<td class="diff-line-num new_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">

508

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python">                <span class="p">(</span><span class="s" style="color: #d14;">"length"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">"count"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">"expect"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">),</span> <span class="p">(</span><span class="s" style="color: #d14;">"max.err"</span><span class="p">,</span><span class="s" style="color: #d14;">""</span><span class="p">),</span></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="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">

509

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python">                <span class="p">(</span><span class="s" style="color: #d14;">"error counts"</span><span class="p">,</span> <span class="n" style="color: #333;">error_header</span><span class="p">)))</span></span>

</pre>

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509

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<td class="diff-line-num new_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">

510

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

<pre style="margin: 0;"> <span id="LC510" class="line" lang="python">        <span class="n" style="color: #333;">hist_printer</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">newline</span><span class="p">()</span></span>

</pre>

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510

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<td class="diff-line-num new_line old" data-linenumber="511" style="width: 35px; color: rgba(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="LC510" 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="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

511

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="511" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

511

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<td class="diff-line-num new_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">

512

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_adjacent_bases</span><span class="p">(</span><span class="n" style="color: #333;">bases</span><span class="p">):</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">

512

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<td class="diff-line-num new_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

513

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

<pre style="margin: 0;"> <span id="LC513" class="line" lang="python">        <span class="s" style="color: #d14;">"""Print a summary of the bases preceding removed adapter sequences.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="513" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

513

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<td class="diff-line-num new_line" data-linenumber="514" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

514

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

<pre style="margin: 0;"> <span id="LC514" class="line" lang="python"><span class="s" style="color: #d14;">        Print a warning if one of the bases is overrepresented and there are</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC515" class="line" lang="python"><span class="s" style="color: #d14;">        at least 20 preceding bases available.</span></span>

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<pre style="margin: 0;">-<span id="LC515" 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="LC516" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python"><span class="s" style="color: #d14;">        Return:</span></span>

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<pre style="margin: 0;"> <span id="LC518" class="line" lang="python"><span class="s" style="color: #d14;">            True if a warning was printed.</span></span>

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<pre style="margin: 0;"> <span id="LC519" 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="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">...</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">@@ -538,19 +539,19 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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<pre style="margin: 0;"> <span id="LC539" 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="LC540" class="line" lang="python">        <span class="n" style="color: #333;">_print</span><span class="p">()</span></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="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;">-<span id="LC541" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC542" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="python">    <span class="n" style="color: #333;">warning</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">pair</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">2</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">paired</span> <span class="k" style="font-weight: 600;">else</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="545" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC545" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapters</span><span class="p">[</span><span class="n" style="color: #333;">pair</span><span class="p">]</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="LC546" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;">-<span id="LC546" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC547" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="548" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC548" class="line" lang="python">        <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"Adapter {}"</span></span>

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<td class="diff-line-num new_line" data-linenumber="549" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC549" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">paired</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="python">            <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"First read: "</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pair</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"Second read: "</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">header</span></span>

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<pre style="margin: 0;">-<span id="LC550" class="line" lang="python"><span class="idiff left right">        </span></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;">for</span> <span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="n" style="color: #333;">adapter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">adapters</span><span class="p">[</span><span class="n" style="color: #333;">pair</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python">            <span class="n" style="color: #333;">_print_title</span><span class="p">(</span><span class="n" style="color: #333;">header</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;">name</span><span class="p">),</span> <span class="n" style="color: #333;">level</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="LC553" class="line" lang="python"><span class="idiff left right">            </span></span>

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<pre style="margin: 0;">+<span id="LC554" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC555" class="line" lang="python">            <span class="n" style="color: #333;">where_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"where"</span><span class="p">][</span><span class="s" style="color: #d14;">"name"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC556" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">where_name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"linked"</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python">                <span class="n" style="color: #333;">front_len</span><span class="p">,</span> <span class="n" style="color: #333;">back_len</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="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">...</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">@@ -576,12 +577,12 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python">                        <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</span><span class="p">]),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC578" class="line" lang="python">                    <span class="n" style="color: #333;">header</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="LC579" class="line" lang="python">                        <span class="s" style="color: #d14;">"Sequence"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Type"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Length"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Trimmed (x)"</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC579" class="line" lang="python"><span class="idiff left right">            </span></span>

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC581" class="line" lang="python">            <span class="n" style="color: #333;">_print</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="582" style="width: 35px; color: rgba(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="LC581" class="line" lang="python"><span class="idiff left right">            </span></span>

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<pre style="margin: 0;">+<span id="LC582" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC583" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"total"</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="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

</td>

<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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<pre style="margin: 0;"> <span id="LC584" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="584" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

584

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<td class="diff-line-num new_line old" data-linenumber="585" style="width: 35px; color: rgba(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="LC584" 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="585" style="width: 35px; color: rgba(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="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

585

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<pre style="margin: 0;">+<span id="LC585" class="line" lang="python"></span>

</pre>

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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">

585

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<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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">where_name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"anywhere"</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">

586

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<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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<pre style="margin: 0;"> <span id="LC587" class="line" lang="python">                <span class="n" style="color: #333;">_print</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_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="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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<pre style="margin: 0;"> <span id="LC588" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"total_front"</span><span class="p">],</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -602,7 +603,7 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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<td class="diff-line-num old_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">

602

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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">

603

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths_back"</span><span class="p">],</span> <span class="n" style="color: #333;">seq_len</span><span class="p">,</span> <span class="n" style="color: #333;">total_records</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_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">

603

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<td class="diff-line-num new_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">

604

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"max_error_rate"</span><span class="p">],</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"errors_back"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num 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">

604

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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;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">'match_probabilities'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

605

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<td class="diff-line-num new_line old" data-linenumber="606" style="width: 35px; color: rgba(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="LC605" 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="606" style="width: 35px; color: rgba(0,0,0,0.3); 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="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

606

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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_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">

606

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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">

607

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<pre style="margin: 0;"> <span id="LC607" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">where_name</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"linked"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_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">

607

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<td class="diff-line-num new_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">

608

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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python">                <span class="n" style="color: #333;">print_error_ranges</span><span class="p">(</span><span class="n" style="color: #333;">front_len</span><span class="p">,</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"front_max_error_rate"</span><span class="p">])</span></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">

608

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<td class="diff-line-num new_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">

609

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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python">                <span class="n" style="color: #333;">print_error_ranges</span><span class="p">(</span><span class="n" style="color: #333;">back_len</span><span class="p">,</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"back_max_error_rate"</span><span class="p">])</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -610,7 +611,7 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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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">

610

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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">

611

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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python">                <span class="n" style="color: #333;">print_histogram</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num old_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">

611

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<td class="diff-line-num new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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

<pre style="margin: 0;"> <span id="LC612" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"front_lengths_front"</span><span class="p">],</span> <span class="n" style="color: #333;">front_len</span><span class="p">,</span> <span class="n" style="color: #333;">total_records</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

</td>

<td class="diff-line-num 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">

613

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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"front_max_error_rate"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="614" style="width: 35px; color: rgba(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="LC613" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"front_errors_front"</span><span class="p">],</span><span class="idiff left right"> </span></span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC614" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"front_errors_front"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

614

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">'front_match_probabilities'</span><span class="p">])</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="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

616

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<pre style="margin: 0;"> <span id="LC616" class="line" lang="python">                <span class="n" style="color: #333;">_print</span><span class="p">()</span></span>

</pre>

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616

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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">

617

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<pre style="margin: 0;"> <span id="LC617" class="line" lang="python">                <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Overview of removed sequences at 3' end:"</span><span class="p">)</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -618,7 +619,7 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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<td class="diff-line-num old_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">

618

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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">

619

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<pre style="margin: 0;"> <span id="LC619" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"back_lengths_back"</span><span class="p">],</span> <span class="n" style="color: #333;">back_len</span><span class="p">,</span> <span class="n" style="color: #333;">total_records</span><span class="p">,</span></span>

</pre>

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619

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<td class="diff-line-num new_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">

620

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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"back_max_error_rate"</span><span class="p">],</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"back_errors_back"</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">

620

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<td class="diff-line-num new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">'back_match_probabilities'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

621

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<td class="diff-line-num new_line old" data-linenumber="622" style="width: 35px; color: rgba(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="LC621" 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="622" style="width: 35px; color: rgba(0,0,0,0.3); 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="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

622

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<pre style="margin: 0;">+<span id="LC622" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

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<td class="diff-line-num new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">where_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"front"</span><span class="p">,</span> <span class="s" style="color: #d14;">"prefix"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

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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="n" style="color: #333;">print_error_ranges</span><span class="p">(</span><span class="n" style="color: #333;">seq_len</span><span class="p">,</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"max_error_rate"</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

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<pre style="margin: 0;"> <span id="LC625" class="line" lang="python">                <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Overview of removed sequences:"</span><span class="p">)</span></span>

</pre>

</td>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -626,7 +627,7 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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<td class="diff-line-num old_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">

626

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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">

627

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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths_front"</span><span class="p">],</span> <span class="n" style="color: #333;">seq_len</span><span class="p">,</span> <span class="n" style="color: #333;">total_records</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_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">

627

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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">

628

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

<pre style="margin: 0;"> <span id="LC628" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"max_error_rate"</span><span class="p">],</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"errors_front"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_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">

628

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<td class="diff-line-num new_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

629

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">'match_probabilities'</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="629" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

629

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<td class="diff-line-num new_line old" data-linenumber="630" style="width: 35px; color: rgba(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="LC629" class="line" lang="python"><span class="idiff left right">            </span></span>

</pre>

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630

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<pre style="margin: 0;">+<span id="LC630" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="630" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

630

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<td class="diff-line-num new_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python">            <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">where_name</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"back"</span><span class="p">,</span> <span class="s" style="color: #d14;">"suffix"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="631" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

631

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<td class="diff-line-num new_line" data-linenumber="632" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

632

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<pre style="margin: 0;"> <span id="LC632" class="line" lang="python">                <span class="n" style="color: #333;">print_error_ranges</span><span class="p">(</span><span class="n" style="color: #333;">seq_len</span><span class="p">,</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"max_error_rate"</span><span class="p">])</span></span>

</pre>

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632

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<td class="diff-line-num new_line" data-linenumber="633" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC633" class="line" lang="python">                <span class="n" style="color: #333;">warning</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">warning</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">print_adjacent_bases</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="636" style="width: 35px; color: rgba(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="637" style="width: 35px; color: rgba(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">@@ -636,7 +637,7 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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<td class="diff-line-num new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC637" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"lengths_back"</span><span class="p">],</span> <span class="n" style="color: #333;">seq_len</span><span class="p">,</span> <span class="n" style="color: #333;">total_records</span><span class="p">,</span></span>

</pre>

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637

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"max_error_rate"</span><span class="p">],</span> <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">"errors_back"</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num new_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">

639

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="python">                    <span class="n" style="color: #333;">adapter</span><span class="p">[</span><span class="s" style="color: #d14;">'match_probabilities'</span><span class="p">])</span></span>

</pre>

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639

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<pre style="margin: 0;">-<span id="LC639" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC640" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

641

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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">warning</span><span class="p">:</span></span>

</pre>

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641

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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">

642

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<pre style="margin: 0;"> <span id="LC642" class="line" lang="python">        <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">'WARNING:'</span><span class="p">)</span></span>

</pre>

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642

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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">

643

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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python">        <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">INDENTED</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">wrap</span><span class="p">(</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="645" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -645,7 +646,7 @@ def print_adapter_report(adapters, outfile, paired, total_records, max_width):</td>

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645

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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">

646

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<pre style="margin: 0;"> <span id="LC646" class="line" lang="python"></span>

</pre>

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646

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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">

647

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<pre style="margin: 0;"> <span id="LC647" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_pre_trim_report</span><span class="p">(</span><span class="n" style="color: #333;">summary</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

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<pre style="margin: 0;"> <span id="LC648" class="line" lang="python">    <span class="s" style="color: #d14;">"""Print pre-trimming stats.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC648" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC649" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC650" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC651" class="line" lang="python"><span class="s" style="color: #d14;">        summary: The summary dict.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC652" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: The output file.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="664" style="width: 35px; color: rgba(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="665" style="width: 35px; color: rgba(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">@@ -664,10 +665,10 @@ def print_pre_trim_report(summary, outfile):</td>

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<pre style="margin: 0;"> <span id="LC665" class="line" lang="python">            <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">"Read {}: {}"</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;">read</span><span class="p">,</span> <span class="n" style="color: #333;">src</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC666" class="line" lang="python">        <span class="n" style="color: #333;">_print</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC667" class="line" lang="python">        <span class="n" style="color: #333;">print_stats_report</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC667" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC668" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC669" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_post_trim_report</span><span class="p">(</span><span class="n" style="color: #333;">summary</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC670" class="line" lang="python">    <span class="s" style="color: #d14;">"""Print post-trimming stats.</span></span>

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<td class="diff-line-num new_line old" data-linenumber="671" style="width: 35px; color: rgba(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="LC670" 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="LC671" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="672" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC672" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="673" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC673" class="line" lang="python"><span class="s" style="color: #d14;">        summary: The summary dict.</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="674" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC674" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: The output file.</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -691,7 +692,7 @@ def print_post_trim_report(summary, outfile):</td>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC692" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_stats_report</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="n" style="color: #333;">outfile</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC694" class="line" lang="python">    <span class="s" style="color: #d14;">"""Print stats.</span></span>

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<pre style="margin: 0;">-<span id="LC694" 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="LC695" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC696" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC697" class="line" lang="python"><span class="s" style="color: #d14;">        data: The stats dict.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC698" class="line" lang="python"><span class="s" style="color: #d14;">        outfile: The output file.</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -703,10 +704,10 @@ def print_stats_report(data, outfile):</td>

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<pre style="margin: 0;"> <span id="LC704" class="line" lang="python">    <span class="n" style="color: #333;">max_width</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">max_count</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC705" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># add space for commas and column separation</span></span>

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<pre style="margin: 0;"> <span id="LC706" class="line" lang="python">    <span class="n" style="color: #333;">max_width</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">max_width</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">3</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="LC706" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC707" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC708" class="line" lang="python">    <span class="n" style="color: #333;">_print_title</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">TitlePrinter</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="python">    <span class="n" style="color: #333;">_print</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">RowPrinter</span><span class="p">(</span><span class="n" style="color: #333;">outfile</span><span class="p">,</span> <span class="p">(</span><span class="mi" style="color: #099;">35</span><span class="p">,</span> <span class="n" style="color: #333;">max_width</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC709" class="line" lang="python"><span class="idiff left right">    </span></span>

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710

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<pre style="margin: 0;">+<span id="LC710" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="710" style="width: 35px; color: rgba(0,0,0,0.3); 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="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">

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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_print_histogram</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">hist1</span><span class="p">,</span> <span class="n" style="color: #333;">hist2</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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711

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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">

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python">        <span class="n" style="color: #333;">_print_title</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="713" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC713" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hist1</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -720,7 +721,7 @@ def print_stats_report(data, outfile):</td>

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<pre style="margin: 0;"> <span id="LC721" class="line" lang="python">            <span class="n" style="color: #333;">hist</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">hist1</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</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="n" style="color: #333;">x</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="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="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;">for</span> <span class="n" style="color: #333;">histbin</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">hist</span><span class="p">:</span></span>

</pre>

</td>

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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

</td>

<td class="diff-line-num new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

723

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<pre style="margin: 0;"> <span id="LC723" class="line" lang="python">            <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">histbin</span><span class="p">)</span></span>

</pre>

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<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="724" style="width: 35px; color: rgba(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="idiff left right">    </span></span>

</pre>

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<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="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">

724

</td>

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

<pre style="margin: 0;">+<span id="LC724" class="line" lang="python"></span>

</pre>

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<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="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

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<pre style="margin: 0;"> <span id="LC725" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_print_base_histogram</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">hist</span><span class="p">,</span> <span class="n" style="color: #333;">extra_width</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="n" style="color: #333;">index_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Pos'</span><span class="p">):</span></span>

</pre>

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<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="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

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

<pre style="margin: 0;"> <span id="LC726" class="line" lang="python">        <span class="n" style="color: #333;">_print_title</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>

</pre>

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<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

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<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC727" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hist</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -734,7 +735,7 @@ def print_stats_report(data, outfile):</td>

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<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="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="nb" style="color: #0086b3;">round</span><span class="p">(</span><span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">*</span> <span class="mi" style="color: #099;">100</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">total_count</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_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="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

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

<pre style="margin: 0;"> <span id="LC736" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">count</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">row</span><span class="p">)</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="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

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<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="n" style="color: #333;">_print</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">base_pcts</span><span class="p">,</span> <span class="n" style="color: #333;">extra_width</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">extra_width</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="737" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

737

</td>

<td class="diff-line-num new_line old" data-linenumber="738" style="width: 35px; color: rgba(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="LC737" 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="738" style="width: 35px; color: rgba(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="738" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

738

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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="LC738" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_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="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

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<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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_print_tile_histogram</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">hist</span><span class="p">):</span></span>

</pre>

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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

</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

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<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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">hist</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num 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

</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;">_print_title</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">2</span><span class="p">)</span></span>

</pre>

</td>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -745,7 +746,7 @@ def print_stats_report(data, outfile):</td>

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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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<pre style="margin: 0;"> <span id="LC746" class="line" lang="python">            <span class="mi" style="color: #099;">4</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</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;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'read1'</span><span class="p">][</span><span class="s" style="color: #d14;">'counts'</span><span class="p">]</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">ncol</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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<pre style="margin: 0;"> <span id="LC747" class="line" lang="python">        <span class="n" style="color: #333;">_print_base_histogram</span><span class="p">(</span></span>

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<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">

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<pre style="margin: 0;"> <span id="LC748" class="line" lang="python">            <span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">hist</span><span class="p">,</span> <span class="n" style="color: #333;">extra_width</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_tile_width</span><span class="p">,</span> <span class="n" style="color: #333;">index_name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Tile'</span><span class="p">)</span></span>

</pre>

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748

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<td class="diff-line-num new_line old" data-linenumber="749" style="width: 35px; color: rgba(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="LC748" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC749" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC750" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_print_tile_base_histogram</span><span class="p">(</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">hist</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC751" class="line" lang="python">        <span class="s" style="color: #d14;">"""Print a histogram of position x tile, with values as the median</span></span>

</pre>

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751

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<pre style="margin: 0;"> <span id="LC752" class="line" lang="python"><span class="s" style="color: #d14;">        base quality.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="768" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -768,9 +769,9 @@ def print_stats_report(data, outfile):</td>

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<pre style="margin: 0;"> <span id="LC769" class="line" lang="python">                    <span class="n" style="color: #333;">weighted_median</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">tile_counts</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC770" class="line" lang="python">                    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">tile_counts</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">tiles</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">values</span><span class="p">()),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC771" class="line" lang="python">                <span class="n" style="color: #333;">extra_width</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">max_tile_width</span><span class="p">)</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC771" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC772" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC773" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span><span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="s" style="color: #d14;">'Read1'</span><span class="p">,</span> <span class="s" style="color: #d14;">'Read2'</span><span class="p">,</span> <span class="n" style="color: #333;">header</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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<td class="diff-line-num new_line old" data-linenumber="774" style="width: 35px; color: rgba(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="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC774" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC775" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Sequence-level stats</span></span>

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<pre style="margin: 0;"> <span id="LC776" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">(</span></span>

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776

</td>

<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC777" class="line" lang="python">        <span class="s" style="color: #d14;">"Read pairs:"</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">paired</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">"Reads:"</span><span class="p">,</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="794" style="width: 35px; color: rgba(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">@@ -793,7 +794,7 @@ def print_stats_report(data, outfile):</td>

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<td class="diff-line-num old_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

</td>

<td class="diff-line-num new_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

794

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

<pre style="margin: 0;"> <span id="LC794" class="line" lang="python">        <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'read1'</span><span class="p">][</span><span class="s" style="color: #d14;">'gc'</span><span class="p">][</span><span class="s" style="color: #d14;">'hist'</span><span class="p">],</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="794" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

794

</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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<pre style="margin: 0;"> <span id="LC795" class="line" lang="python">        <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'read2'</span><span class="p">][</span><span class="s" style="color: #d14;">'gc'</span><span class="p">][</span><span class="s" style="color: #d14;">'hist'</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_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

</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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<pre style="margin: 0;"> <span id="LC796" class="line" lang="python">    <span class="n" style="color: #333;">_print</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="796" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

796

</td>

<td class="diff-line-num new_line old" data-linenumber="797" style="width: 35px; color: rgba(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="LC796" 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="797" style="width: 35px; color: rgba(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="797" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

797

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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="LC797" class="line" lang="python"></span>

</pre>

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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

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<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

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<pre style="margin: 0;"> <span id="LC798" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'tile_sequence_qualities'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'read1'</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

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<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

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<pre style="margin: 0;"> <span id="LC799" class="line" lang="python">        <span class="n" style="color: #333;">_print_tile_histogram</span><span class="p">(</span></span>

</pre>

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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="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="s" style="color: #d14;">"Read 1 per-tile sequence qualities (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">)"</span><span class="p">,</span></span>

</pre>

</td>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -803,7 +804,7 @@ def print_stats_report(data, outfile):</td>

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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="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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<pre style="margin: 0;"> <span id="LC804" class="line" lang="python">            <span class="s" style="color: #d14;">"Read 2 per-tile sequence qualities (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">)"</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="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

805

</td>

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

<pre style="margin: 0;"> <span id="LC805" class="line" lang="python">            <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'read2'</span><span class="p">][</span><span class="s" style="color: #d14;">'tile_sequence_qualities'</span><span class="p">])</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="805" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

805

</td>

<td class="diff-line-num new_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

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

<pre style="margin: 0;"> <span id="LC806" class="line" lang="python">        <span class="n" style="color: #333;">_print</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="806" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

806

</td>

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

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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="LC806" 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="807" style="width: 35px; color: rgba(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="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

807

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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="LC807" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="807" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

807

</td>

<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC808" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Base-level stats</span></span>

</pre>

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<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="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

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

<pre style="margin: 0;"> <span id="LC809" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">'base_qualities'</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">data</span><span class="p">[</span><span class="s" style="color: #d14;">'read1'</span><span class="p">]:</span></span>

</pre>

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

<pre style="margin: 0;"> <span id="LC810" class="line" lang="python">        <span class="n" style="color: #333;">_print_base_histogram</span><span class="p">(</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -835,7 +836,7 @@ def print_stats_report(data, outfile):</td>

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<pre style="margin: 0;"> <span id="LC836" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sizeof</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">seps</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">True</span><span class="p">,</span> <span class="n" style="color: #333;">prec</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="LC837" class="line" lang="python">    <span class="s" style="color: #d14;">"""Returns the largest string size of all objects in x, where x is a</span></span>

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<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

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<pre style="margin: 0;"> <span id="LC838" class="line" lang="python"><span class="s" style="color: #d14;">    sequence of string or numeric values.</span></span>

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<pre style="margin: 0;">-<span id="LC838" 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="LC839" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="840" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC840" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<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">

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<pre style="margin: 0;"> <span id="LC841" class="line" lang="python"><span class="s" style="color: #d14;">        *x: The objects to test.</span></span>

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<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

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<pre style="margin: 0;"> <span id="LC842" class="line" lang="python"><span class="s" style="color: #d14;">        seps: Whether to include separators (,.) in the size.</span></span>

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<br>

</li>

<li id="f88c7193047348563d4cfabf2ec77be4c615e6e7">

<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#f88c7193047348563d4cfabf2ec77be4c615e6e7"><strong>atropos/io/seqio.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -11,9 +11,9 @@ from atropos.io import STDOUT, xopen</td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">atropos.io.compression</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">splitext_compressed</span></span>

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<pre style="margin: 0;"> <span id="LC12" 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="n" style="color: #333;">Summarizable</span><span class="p">,</span> <span class="n" style="color: #333;">truncate_string</span><span class="p">,</span> <span class="n" style="color: #333;">ALPHABETS</span></span>

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

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<td class="diff-line-num new old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"><span class="n" style="color: #333;">SINGLE</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="LC15" class="line" lang="python"><span class="n" style="color: #333;">READ1</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="LC16" class="line" lang="python"><span class="n" style="color: #333;">READ2</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">2</span></span>

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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"><span class="n" style="color: #333;">SINGLE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">READ1</span></span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="python"><span class="n" style="color: #333;">PAIRED</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="o" style="font-weight: 600;">|</span><span class="mi" style="color: #099;">2</span></span>

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

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19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">FormatError</span><span class="p">(</span><span class="n" style="color: #333;">AtroposError</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1045" style="width: 35px; color: rgba(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="1045" style="width: 35px; color: rgba(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">@@ -1045,16 +1045,16 @@ def get_format(</td>

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<td class="diff-line-num new_line" data-linenumber="1045" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1045

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<pre style="margin: 0;"> <span id="LC1045" class="line" lang="python">        <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">qualities</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1046

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<td class="diff-line-num new_line" data-linenumber="1046" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1046

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<pre style="margin: 0;"> <span id="LC1046" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Same, but we know that we want to write reads without qualities.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1047

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<td class="diff-line-num new_line" data-linenumber="1047" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1047

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<pre style="margin: 0;"> <span id="LC1047" class="line" lang="python">            <span class="n" style="color: #333;">file_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'fasta'</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); 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="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1048

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<pre style="margin: 0;">+<span id="LC1048" 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="1048" style="width: 35px; color: rgba(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="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1049

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<pre style="margin: 0;">+<span id="LC1049" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownFileType</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not determine file type."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1048" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1048

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<td class="diff-line-num new_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1050

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<pre style="margin: 0;"> <span id="LC1050" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1049" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1049

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<td class="diff-line-num new_line old" data-linenumber="1051" style="width: 35px; color: rgba(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="LC1049" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_format</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="1050" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1050

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<td class="diff-line-num new_line old" data-linenumber="1051" style="width: 35px; color: rgba(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="LC1050" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">UnknownFileType</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not determine file type."</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); 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="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1051

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<pre style="margin: 0;">+<span id="LC1051" class="line" lang="python">    <span class="n" style="color: #333;">file_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1051" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1051

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<td class="diff-line-num new_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1052

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<pre style="margin: 0;"> <span id="LC1052" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1052" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1052

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<td class="diff-line-num new_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1053

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<pre style="margin: 0;"> <span id="LC1053" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'fastq'</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">qualities</span> <span class="ow" style="font-weight: 600;">is</span> <span class="bp" style="color: #999;">False</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="1053" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1053

</td>

<td class="diff-line-num new_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1054

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<pre style="margin: 0;"> <span id="LC1054" 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>

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<td class="diff-line-num old_line" data-linenumber="1054" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1054

</td>

<td class="diff-line-num new_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1055

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<pre style="margin: 0;"> <span id="LC1055" class="line" lang="python">            <span class="s" style="color: #d14;">"Output format cannot be FASTQ since no quality values are "</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1055" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1055

</td>

<td class="diff-line-num new_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1056

</td>

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<pre style="margin: 0;"> <span id="LC1056" class="line" lang="python">            <span class="s" style="color: #d14;">"available."</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1056" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1056

</td>

<td class="diff-line-num new_line" data-linenumber="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1057

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<pre style="margin: 0;"> <span id="LC1057" class="line" lang="python"></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="1057" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1057

</td>

<td class="diff-line-num new_line old" data-linenumber="1058" style="width: 35px; color: rgba(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="LC1057" class="line" lang="python">    <span class="n" style="color: #333;">file_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">file_format</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lower</span><span class="p">()</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1058

</td>

<td class="diff-line-num new_line" data-linenumber="1058" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1058

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

<pre style="margin: 0;"> <span id="LC1058" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_format</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'fasta'</span><span class="p">:</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="1059" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1059

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<pre style="margin: 0;"> <span id="LC1059" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">colorspace</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC1060" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">ColorspaceFastaFormat</span><span class="p">(</span><span class="n" style="color: #333;">line_length</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="1fb9116d8cf0c1b4d5121d2b653391d84b794ac6">

<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#1fb9116d8cf0c1b4d5121d2b653391d84b794ac6"><strong>atropos/util/__init__.py</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,23 +25,23 @@ class Alphabet():</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">            <span class="n" style="color: #333;">valid_characters</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;">default_character</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC26" 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;">valid_characters</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">valid_characters</span></span>

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<pre style="margin: 0;"> <span id="LC27" 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;">default_character</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">default_character</span></span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"><span class="idiff left right">    </span></span>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__contains__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">character</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">character</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;">valid_characters</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">validate</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">character</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python">        <span class="s" style="color: #d14;">"""Raises NotInAlphabetError if the character is not in the alphabet.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC34" 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="35" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC35" 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;">character</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); 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="36" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC36" class="line" lang="python">            <span class="k" style="font-weight: 600;">raise</span> <span class="n" style="color: #333;">NotInAlphabetError</span><span class="p">(</span><span class="n" style="color: #333;">character</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">validate_string</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python">        <span class="s" style="color: #d14;">"""Raises NotInAlphabetError if any character in 'string' is not in the</span></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;">        alphabet.</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">character</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">string</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC43" 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;">validate</span><span class="p">(</span><span class="n" style="color: #333;">character</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python"><span class="idiff left right">        </span></span>

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

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">resolve</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">character</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns 'character' if it's in the alphabet, otherwise the</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"><span class="s" style="color: #d14;">        alphabet's default character.</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="50" style="width: 35px; color: rgba(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">@@ -50,7 +50,7 @@ class Alphabet():</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">character</span></span>

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<pre style="margin: 0;"> <span id="LC51" 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="LC52" 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;">default_character</span></span>

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<pre style="margin: 0;">-<span id="LC53" 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="54" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC53" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">resolve_string</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">string</span><span class="p">):</span></span>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns a new string with any non-alphabet characters replaced</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="s" style="color: #d14;">        with the default character.</span></span>

</pre>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,7 +103,7 @@ LOG2 = math.log(2)</td>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">RandomMatchProbability</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="LC104" class="line" lang="python">    <span class="s" style="color: #d14;">"""Class for computing random match probability for DNA sequences based on</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="s" style="color: #d14;">    binomial expectation. Maintains a cache of factorials to speed computation.</span></span>

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<pre style="margin: 0;">-<span id="LC106" 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="LC106" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python"><span class="s" style="color: #d14;">        init_size: Initial cache size.</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC112" 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;">factorials</span> <span class="o" style="font-weight: 600;">=</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;">init_size</span></span>

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<pre style="margin: 0;"> <span id="LC113" 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;">max_n</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="LC114" 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;">cur_array_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">init_size</span></span>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC116" 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 class="n" style="color: #333;">matches</span><span class="p">,</span> <span class="n" style="color: #333;">size</span><span class="p">,</span> <span class="n" style="color: #333;">match_prob</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.25</span><span class="p">,</span> <span class="n" style="color: #333;">mismatch_prob</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.75</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="python">        <span class="s" style="color: #d14;">"""Computes the random-match probability for a given sequence size and</span></span>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;">        number of matches.</span></span>

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<pre style="margin: 0;">-<span id="LC119" 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="LC119" class="line" lang="python"></span>

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

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python"><span class="s" style="color: #d14;">            match_prob: Probability of two random bases matching.</span></span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python"><span class="s" style="color: #d14;">            mismatch_prob: Probability of two random bases not matcing.</span></span>

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<pre style="margin: 0;">-<span id="LC123" 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="LC123" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="python"><span class="s" style="color: #d14;">        Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python"><span class="s" style="color: #d14;">            The probability.</span></span>

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<pre style="margin: 0;"> <span id="LC126" 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">@@ -129,17 +129,17 @@ class RandomMatchProbability(object):</td>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="python">        <span class="n" style="color: #333;">prob</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;">cache</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;">key</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">prob</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">prob</span></span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"><span class="idiff left right">        </span></span>

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

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># When there are no mismatches, the probability is</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># just that of observing a specific sequence of the</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># given length by chance.</span></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">matches</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">size</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python">            <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">match_prob</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="LC138" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC138" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC139" 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="LC140" class="line" lang="python">            <span class="n" style="color: #333;">nfac</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;">factorial</span><span class="p">(</span><span class="n" style="color: #333;">size</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python">            <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="python"><span class="idiff left right">            </span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC143" 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="n" style="color: #333;">matches</span><span class="p">,</span> <span class="n" style="color: #333;">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="LC144" class="line" lang="python">                <span class="n" style="color: #333;">j</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">size</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">i</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;"># use integer division in the case that the numbers are too</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="149" style="width: 35px; color: rgba(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">@@ -149,10 +149,10 @@ class RandomMatchProbability(object):</td>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">OverflowError</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python">                    <span class="n" style="color: #333;">div</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nfac</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;">factorial</span><span class="p">(</span><span class="n" style="color: #333;">i</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;">factorial</span><span class="p">(</span><span class="n" style="color: #333;">j</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC151" class="line" lang="python">                <span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">+=</span> <span class="p">(</span><span class="n" style="color: #333;">mismatch_prob</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">j</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="p">(</span><span class="n" style="color: #333;">match_prob</span> <span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">div</span></span>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"></span>

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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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<pre style="margin: 0;"> <span id="LC153" 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;">cache</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">prob</span></span>

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">prob</span></span>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">factorial</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">num</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns `num`!.</span></span>

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<pre style="margin: 0;"> <span id="LC158" 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">@@ -191,23 +191,23 @@ class Summarizable(object):</td>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="p">(</span><span class="n" style="color: #333;">Mergeable</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;">"""A :class:`Mergeable` that is a constant value. Merging simply checks</span></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"><span class="s" style="color: #d14;">    that two values are identical.</span></span>

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<pre style="margin: 0;">-<span id="LC194" 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="LC194" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python"><span class="s" style="color: #d14;">        value: The value to treat as a constant.</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC198" 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 class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">value</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC199" 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;">value</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="python">        <span class="s" style="color: #d14;">"""Check that `self==other`.</span></span>

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<pre style="margin: 0;">-<span id="LC203" 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="LC203" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"><span class="s" style="color: #d14;">        Raises:</span></span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"><span class="s" style="color: #d14;">            ValueError</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC207" 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;">other</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC208" 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;">"{} != {}"</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__eq__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</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;">"""Returns True if `self.value==other` (or `other.value` if `other` is</span></span>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;">        a :class:`Const`).</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="215" style="width: 35px; color: rgba(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">@@ -215,7 +215,7 @@ class Const(Mergeable):</td>

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">Const</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python">            <span class="n" style="color: #333;">other</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">value</span></span>

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<pre style="margin: 0;"> <span id="LC217" 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;">value</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">other</span></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python"><span class="idiff left right">    </span></span>

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

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<pre style="margin: 0;"> <span id="LC219" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__repr__</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="LC220" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">str</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;">value</span><span class="p">)</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="LC224" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC225" 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 class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC226" 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;">dtime</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datetime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">now</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC227" 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;"><span class="idiff left">clock</span></span><span class="idiff"> </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">time</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">clock</span></span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC227" 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;"><span class="idiff left">process_time</span></span><span class="idiff"> </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">time</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">process_time</span></span><span class="p">()</span></span>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC229" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">timestamp</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="LC230" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns the unix timestamp.</span></span>

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<pre style="margin: 0;"> <span id="LC231" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC232" 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;">dtime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python"><span class="idiff left right">    </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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">isoformat</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="LC235" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns the datetime in ISO format.</span></span>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC237" 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;">dtime</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isoformat</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__sub__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">minval</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.01</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python">        <span class="s" style="color: #d14;">"""Subtract another timestamp from this one.</span></span>

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<pre style="margin: 0;">-<span id="LC241" 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="LC241" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python"><span class="s" style="color: #d14;">        Args:</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"><span class="s" style="color: #d14;">            other: The other timestamp.</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"><span class="s" style="color: #d14;">            minval: The minimum difference.</span></span>

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<pre style="margin: 0;">-<span id="LC245" 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="LC245" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC246" class="line" lang="python"><span class="s" style="color: #d14;">        Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC247" class="line" lang="python"><span class="s" style="color: #d14;">            A dict of {wallclock=<datetime_diff>, cpu=<clock_diff>}.</span></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC249" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="python">            <span class="n" style="color: #333;">wallclock</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">minval</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;">timestamp</span><span class="p">()</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">timestamp</span><span class="p">()),</span></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python">            <span class="n" style="color: #333;">cpu</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">minval</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;"><span class="idiff left">clock</span></span><span class="idiff"> </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">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">clock</span></span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC251" class="line" lang="python">            <span class="n" style="color: #333;">cpu</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">minval</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;"><span class="idiff left">process_time</span></span><span class="idiff"> </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">other</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">process_time</span></span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Timing</span><span class="p">(</span><span class="n" style="color: #333;">Summarizable</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python">    <span class="s" style="color: #d14;">"""Context manager that maintains timing information using</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">@@ -258,19 +258,19 @@ class Timing(Summarizable):</td>

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<pre style="margin: 0;"> <span id="LC258" 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 class="bp" style="color: #999;">self</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC259" 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;">start_time</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="LC260" 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;">cur_time</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="LC261" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__enter__</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="LC263" 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;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Timestamp</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

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<pre style="margin: 0;">-<span id="LC265" 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="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__exit__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">exception_type</span><span class="p">,</span> <span class="n" style="color: #333;">exception_value</span><span class="p">,</span> <span class="n" style="color: #333;">traceback</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC267" 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;">update</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC268" class="line" lang="python"><span class="idiff left right">    </span></span>

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

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">update</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="LC270" class="line" lang="python">        <span class="s" style="color: #d14;">"""Set :attr:`self.cur_time` to the current time.</span></span>

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC272" 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;">cur_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">Timestamp</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC273" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC274" 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="LC275" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns a summary dict</span></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="python"><span class="s" style="color: #d14;">        {start=<start_time>, wallclock=<datetime_diff>, cpu=<clock_diff>}.</span></span>

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<pre style="margin: 0;"> <span id="LC284" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">CountingDict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">,</span> <span class="n" style="color: #333;">Mergeable</span><span class="p">,</span> <span class="n" style="color: #333;">Summarizable</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python">    <span class="s" style="color: #d14;">"""A dictionary that always returns 0 on get of a missing key.</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"><span class="s" style="color: #d14;">        sort_by: Whether summary is sorted by key (0) or value (1).</span></span>

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<pre style="margin: 0;"> <span id="LC290" 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="295" style="width: 35px; color: rgba(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="295" style="width: 35px; color: rgba(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">@@ -295,15 +295,15 @@ class CountingDict(dict, Mergeable, Summarizable):</td>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">keys</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">keys</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC297" 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;">increment</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC299" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC300" 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;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</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="LC301" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC302" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">increment</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">inc</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="LC303" class="line" lang="python">        <span class="s" style="color: #d14;">"""Increment the count of `key` by `inc`.</span></span>

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<pre style="margin: 0;"> <span id="LC304" class="line" lang="python"><span class="s" style="color: #d14;">        """</span></span>

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python">        <span class="bp" style="color: #999;">self</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">inc</span></span>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">CountingDict</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC309" 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>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="311" style="width: 35px; color: rgba(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">@@ -311,13 +311,13 @@ class CountingDict(dict, Mergeable, Summarizable):</td>

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<pre style="margin: 0;"> <span id="LC311" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">other</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC312" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">value</span></span>

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<pre style="margin: 0;"> <span id="LC313" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">self</span></span>

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<pre style="margin: 0;">-<span id="LC314" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC314" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_sorted_items</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="LC316" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns an iterable of (key, value) sorted according to this</span></span>

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<pre style="margin: 0;"> <span id="LC317" class="line" lang="python"><span class="s" style="color: #d14;">        CountingDict's `sort_by` param.</span></span>

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

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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">sorted</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;">items</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;">item</span><span class="p">:</span> <span class="n" style="color: #333;">item</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;">sort_by</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC321" 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="LC322" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns an OrderedDict of sorted items.</span></span>

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<pre style="margin: 0;"> <span id="LC323" 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="332" style="width: 35px; color: rgba(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">@@ -332,7 +332,7 @@ class Histogram(CountingDict):</td>

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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="python">            <span class="n" style="color: #333;">hist</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">hist</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python">            <span class="n" style="color: #333;">summary</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_summary_stats</span><span class="p">())</span></span>

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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"><span class="idiff left right">    </span></span>

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

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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_summary_stats</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="LC337" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns dict with mean, median, and modes of histogram.</span></span>

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<pre style="margin: 0;"> <span id="LC338" 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="347" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -347,19 +347,19 @@ class Histogram(CountingDict):</td>

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

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">NestedDict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">dict</span><span class="p">,</span> <span class="n" style="color: #333;">Mergeable</span><span class="p">,</span> <span class="n" style="color: #333;">Summarizable</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC349" class="line" lang="python">    <span class="s" style="color: #d14;">"""A dict that initalizes :class:`CountingDict`s for missing keys.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC350" 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="LC350" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC351" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC352" class="line" lang="python"><span class="s" style="color: #d14;">        shape: The flattened shape: 'long' or 'wide'.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC353" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC354" 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 class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">shape</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"wide"</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC355" 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>

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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;">shape</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shape</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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<pre style="margin: 0;">+<span id="LC357" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC358" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__getitem__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">name</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">name</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</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="LC360" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">[</span><span class="n" style="color: #333;">name</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">CountingDict</span><span class="p">()</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC361" 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;">get</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC362" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="python">    <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">other</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">other</span><span class="p">,</span> <span class="n" style="color: #333;">NestedDict</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;">raise</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">(</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -370,10 +370,10 @@ class NestedDict(dict, Mergeable, Summarizable):</td>

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<pre style="margin: 0;"> <span id="LC370" 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="LC371" class="line" lang="python">                <span class="bp" style="color: #999;">self</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">value</span></span>

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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;">self</span></span>

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<pre style="margin: 0;">-<span id="LC373" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC373" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC374" 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="LC375" class="line" lang="python">        <span class="s" style="color: #d14;">"""Returns a flattened version of the nested dict.</span></span>

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<pre style="margin: 0;">-<span id="LC376" 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="LC376" class="line" lang="python"></span>

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

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<pre style="margin: 0;"> <span id="LC378" class="line" lang="python"><span class="s" style="color: #d14;">            When `shape=='long'`, a list of (key1, key2, value) tuples.</span></span>

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="python"><span class="s" style="color: #d14;">            When `shape=='wide'`, a dict of</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="410" style="width: 35px; color: rgba(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">@@ -410,11 +410,11 @@ def merge_dicts(dest, src):</td>

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<pre style="margin: 0;"> <span id="LC410" class="line" lang="python">    <span class="s" style="color: #d14;">"""Merge corresponding items in `src` into `dest`. Values in `src` missing</span></span>

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<pre style="margin: 0;"> <span id="LC411" class="line" lang="python"><span class="s" style="color: #d14;">    in `dest` are simply added to `dest`. Values that appear in both `src` and</span></span>

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<pre style="margin: 0;"> <span id="LC412" class="line" lang="python"><span class="s" style="color: #d14;">    `dest` are merged using `merge_values`.</span></span>

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<pre style="margin: 0;">-<span id="LC413" 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="LC413" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC414" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC415" class="line" lang="python"><span class="s" style="color: #d14;">        dest: The dict to merge into.</span></span>

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<pre style="margin: 0;"> <span id="LC416" class="line" lang="python"><span class="s" style="color: #d14;">        src: The dict to merge from.</span></span>

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

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<pre style="margin: 0;"> <span id="LC418" class="line" lang="python"><span class="s" style="color: #d14;">    Raises:</span></span>

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<pre style="margin: 0;"> <span id="LC419" class="line" lang="python"><span class="s" style="color: #d14;">        ValueError if a value is not one of the accepted types.</span></span>

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<pre style="margin: 0;"> <span id="LC420" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC426" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC427" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">merge_values</span><span class="p">(</span><span class="n" style="color: #333;">v_dest</span><span class="p">,</span> <span class="n" style="color: #333;">v_src</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC428" class="line" lang="python">    <span class="s" style="color: #d14;">"""Merge two values based on their types, as follows:</span></span>

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<pre style="margin: 0;">-<span id="LC429" 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="LC429" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC430" class="line" lang="python"><span class="s" style="color: #d14;">    - Mergeable: merging is done by the dest object's merge function.</span></span>

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<pre style="margin: 0;"> <span id="LC431" class="line" lang="python"><span class="s" style="color: #d14;">    - dict: merge_dicts is called recursively.</span></span>

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<pre style="margin: 0;"> <span id="LC432" class="line" lang="python"><span class="s" style="color: #d14;">    - Number: values are summed.</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">@@ -434,11 +434,11 @@ def merge_values(v_dest, v_src):</td>

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<pre style="margin: 0;"> <span id="LC434" class="line" lang="python"><span class="s" style="color: #d14;">    they must be the same length. Then, corresponding values are handled as</span></span>

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<pre style="margin: 0;"> <span id="LC435" class="line" lang="python"><span class="s" style="color: #d14;">    above. The value is returned as a list.</span></span>

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<pre style="margin: 0;"> <span id="LC436" class="line" lang="python"><span class="s" style="color: #d14;">    - Otherwise: Treated as a Const (i.e. must be identical).</span></span>

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<pre style="margin: 0;">-<span id="LC437" 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="LC437" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC439" class="line" lang="python"><span class="s" style="color: #d14;">        v_dest: The dest value.</span></span>

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="python"><span class="s" style="color: #d14;">        v_src: The src value.</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="LC441" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="python"><span class="s" style="color: #d14;">        The merged value.</span></span>

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<pre style="margin: 0;"> <span id="LC444" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC482" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC483" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">sequence_complexity</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="LC484" class="line" lang="python">    <span class="s" style="color: #d14;">"""Computes a simple measure of sequence complexity.</span></span>

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<pre style="margin: 0;">-<span id="LC485" 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="LC485" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC487" class="line" lang="python"><span class="s" style="color: #d14;">        seq: The sequence to measure.</span></span>

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<pre style="margin: 0;">-<span id="LC488" 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="LC488" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC490" class="line" lang="python"><span class="s" style="color: #d14;">        Complexity, as a value [0,2], where 0 = a homopolymer and</span></span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="python"><span class="s" style="color: #d14;">        2 = completely random.</span></span>

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<pre style="margin: 0;"> <span id="LC502" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC503" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">qual2int</span><span class="p">(</span><span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">33</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC504" class="line" lang="python">    <span class="s" style="color: #d14;">"""Convert a quality charater to a phred-scale int.</span></span>

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<pre style="margin: 0;">-<span id="LC505" 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="LC505" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC507" class="line" lang="python"><span class="s" style="color: #d14;">        q: The quality value.</span></span>

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="python"><span class="s" style="color: #d14;">        base: The offset of the first quality value (Old Illumina = 64,</span></span>

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="python"><span class="s" style="color: #d14;">            new Illumina = 33).</span></span>

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<pre style="margin: 0;">-<span id="LC510" 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="LC510" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC511" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC512" class="line" lang="python"><span class="s" style="color: #d14;">        The integer quality.</span></span>

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<pre style="margin: 0;"> <span id="LC513" 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="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">...</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">@@ -515,12 +515,12 @@ def qual2int(qual, base=33):</td>

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

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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;">quals2ints</span><span class="p">(</span><span class="n" style="color: #333;">quals</span><span class="p">,</span> <span class="n" style="color: #333;">base</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">33</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC517" class="line" lang="python">    <span class="s" style="color: #d14;">"""Convert an iterable of quality characters to phred-scale ints.</span></span>

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<pre style="margin: 0;">-<span id="LC518" 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="LC518" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC519" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC520" class="line" lang="python"><span class="s" style="color: #d14;">        quals: The qualities.</span></span>

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<pre style="margin: 0;"> <span id="LC521" class="line" lang="python"><span class="s" style="color: #d14;">        base: The offset of the first quality value (Old Illumina = 64,</span></span>

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<pre style="margin: 0;"> <span id="LC522" class="line" lang="python"><span class="s" style="color: #d14;">            new Illumina = 33).</span></span>

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<pre style="margin: 0;">-<span id="LC523" 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="LC523" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC524" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC525" class="line" lang="python"><span class="s" style="color: #d14;">        A tuple of integer qualities.</span></span>

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<pre style="margin: 0;"> <span id="LC526" 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">@@ -533,14 +533,14 @@ def qual2prob(qchar):</td>

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<pre style="margin: 0;"> <span id="LC533" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC534" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">enumerate_range</span><span class="p">(</span><span class="n" style="color: #333;">collection</span><span class="p">,</span> <span class="n" style="color: #333;">start</span><span class="p">,</span> <span class="n" style="color: #333;">end</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC535" class="line" lang="python">    <span class="s" style="color: #d14;">"""Generates an indexed series:  (0,coll[0]), (1,coll[1]) ...</span></span>

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

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<pre style="margin: 0;"> <span id="LC537" class="line" lang="python"><span class="s" style="color: #d14;">    Only up to (start-end+1) items will be yielded.</span></span>

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<pre style="margin: 0;">-<span id="LC538" 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="LC538" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC539" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC540" class="line" lang="python"><span class="s" style="color: #d14;">        collection: The collection to enumerate.</span></span>

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541

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541

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="python"><span class="s" style="color: #d14;">        start: The starting index.</span></span>

</pre>

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542

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542

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="python"><span class="s" style="color: #d14;">        end: The ending index.</span></span>

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543

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<pre style="margin: 0;">-<span id="LC543" 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="LC543" class="line" lang="python"></span>

</pre>

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544

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544

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<pre style="margin: 0;"> <span id="LC544" class="line" lang="python"><span class="s" style="color: #d14;">    Yields:</span></span>

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545

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="python"><span class="s" style="color: #d14;">        (index, item) tuples.</span></span>

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<pre style="margin: 0;"> <span id="LC546" 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="552" style="width: 35px; color: rgba(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">@@ -552,10 +552,10 @@ def enumerate_range(collection, start, end):</td>

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<pre style="margin: 0;"> <span id="LC552" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC553" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mean</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC554" class="line" lang="python">    <span class="s" style="color: #d14;">"""Computes the mean of a sequence of numeric values.</span></span>

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<pre style="margin: 0;">-<span id="LC555" 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="LC555" class="line" lang="python"></span>

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

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<pre style="margin: 0;"> <span id="LC557" class="line" lang="python"><span class="s" style="color: #d14;">        values: Sequence of numeric values.</span></span>

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558

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<pre style="margin: 0;">-<span id="LC558" 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="LC558" 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">

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<td class="diff-line-num new_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">

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<pre style="margin: 0;"> <span id="LC559" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

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<td class="diff-line-num old_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="s" style="color: #d14;">        The mean (floating point).</span></span>

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<pre style="margin: 0;"> <span id="LC561" 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">@@ -565,10 +565,10 @@ def mean(values):</td>

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<pre style="margin: 0;"> <span id="LC565" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC566" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">weighted_mean</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="python">    <span class="s" style="color: #d14;">"""Computes the mean of a sequence of numeric values weighted by counts.</span></span>

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<pre style="margin: 0;">-<span id="LC568" 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="LC568" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC569" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"><span class="s" style="color: #d14;">        values: Sequence of numeric values.</span></span>

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571

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<pre style="margin: 0;">-<span id="LC571" 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="LC571" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC573" class="line" lang="python"><span class="s" style="color: #d14;">        The weighted mean (floating point).</span></span>

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<pre style="margin: 0;"> <span id="LC574" 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="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">...</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">@@ -606,26 +606,26 @@ def weighted_stdev(values, counts, mu0=None):</td>

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<pre style="margin: 0;"> <span id="LC606" class="line" lang="python">        <span class="n" style="color: #333;">mu0</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">weighted_mean</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC607" 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;">sqrt</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python">        <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span></span>

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<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(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="LC609" class="line" lang="python">            <span class="p">((</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mu0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">count</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new_line old" data-linenumber="609" style="width: 35px; color: rgba(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="LC610" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">count</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">))</span> <span class="o" style="font-weight: 600;">/</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC609" class="line" lang="python">            <span class="p">((</span><span class="n" style="color: #333;">val</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">mu0</span><span class="p">)</span> <span class="o" style="font-weight: 600;">**</span> <span class="mi" style="color: #099;">2</span><span class="p">)</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">count</span></span>

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<pre style="margin: 0;">+<span id="LC610" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">val</span><span class="p">,</span> <span class="n" style="color: #333;">count</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">))</span> <span class="o" style="font-weight: 600;">/</span></span>

</pre>

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611

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611

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<pre style="margin: 0;"> <span id="LC611" class="line" lang="python">        <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">counts</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<td class="diff-line-num new_line" data-linenumber="612" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

612

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<pre style="margin: 0;"> <span id="LC612" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_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">

613

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613

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<pre style="margin: 0;"> <span id="LC613" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">median</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="614" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

614

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<pre style="margin: 0;"> <span id="LC614" class="line" lang="python">    <span class="s" style="color: #d14;">"""Median function borrowed from python statistics module, and sped up by</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="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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<pre style="margin: 0;"> <span id="LC615" class="line" lang="python"><span class="s" style="color: #d14;">    in-place sorting of the array.</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">

616

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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="LC616" 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 old_line" data-linenumber="617" style="width: 35px; color: rgba(0,0,0,0.3); 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="616" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

616

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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="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">

617

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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">

617

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<pre style="margin: 0;"> <span id="LC617" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

</pre>

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<td class="diff-line-num old_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">

618

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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">

618

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<pre style="margin: 0;"> <span id="LC618" class="line" lang="python"><span class="s" style="color: #d14;">        data: Sequence of numeric values.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

619

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<td class="diff-line-num new_line old" data-linenumber="619" style="width: 35px; color: rgba(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="LC619" 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 old_line" data-linenumber="620" style="width: 35px; color: rgba(0,0,0,0.3); 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="619" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

619

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<pre style="margin: 0;">+<span id="LC619" class="line" lang="python"></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">

620

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<td class="diff-line-num new_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">

620

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<pre style="margin: 0;"> <span id="LC620" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

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<td class="diff-line-num new_line" data-linenumber="621" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

621

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<pre style="margin: 0;"> <span id="LC621" class="line" lang="python"><span class="s" style="color: #d14;">        The median (floating point).</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

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<td class="diff-line-num new_line" data-linenumber="622" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

622

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<pre style="margin: 0;"> <span id="LC622" 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="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

</td>

<td class="diff-line-num new_line" data-linenumber="623" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

623

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<pre style="margin: 0;"> <span id="LC623" class="line" lang="python">    <span class="n" style="color: #333;">datalen</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;">values</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_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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<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="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">datalen</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="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

</td>

<td class="diff-line-num new_line" data-linenumber="625" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

625

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

<pre style="margin: 0;"> <span id="LC625" 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;">"Cannot determine the median of an empty sequence"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="626" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

626

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<td class="diff-line-num new_line old" data-linenumber="626" style="width: 35px; color: rgba(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="LC626" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC626" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC627" class="line" lang="python">    <span class="n" style="color: #333;">values</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sort</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC628" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC628" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC629" class="line" lang="python">    <span class="n" style="color: #333;">idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">datalen</span> <span class="o" style="font-weight: 600;">//</span> <span class="mi" style="color: #099;">2</span></span>

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<pre style="margin: 0;"> <span id="LC630" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">datalen</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;">1</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC631" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">values</span><span class="p">[</span><span class="n" style="color: #333;">idx</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">@@ -634,12 +634,12 @@ def median(values):</td>

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<pre style="margin: 0;"> <span id="LC634" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC635" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">weighted_median</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="n" style="color: #333;">counts</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC636" class="line" lang="python">    <span class="s" style="color: #d14;">"""Compute the median of `values` weighted by `counts`.</span></span>

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<pre style="margin: 0;">-<span id="LC637" 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="LC637" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC638" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="python"><span class="s" style="color: #d14;">        values: Sequence of unique values.</span></span>

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="python"><span class="s" style="color: #d14;">        counts: Sequence of counts, where each count is the number of times the</span></span>

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<pre style="margin: 0;"> <span id="LC641" class="line" lang="python"><span class="s" style="color: #d14;">            value at the corresponding position appears in the sample.</span></span>

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<pre style="margin: 0;">-<span id="LC642" 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="LC642" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC643" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

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<pre style="margin: 0;"> <span id="LC644" class="line" lang="python"><span class="s" style="color: #d14;">        The weighted median.</span></span>

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<pre style="margin: 0;"> <span id="LC645" 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">@@ -711,16 +711,16 @@ def truncate_string(string, max_len=100):</td>

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<pre style="margin: 0;"> <span id="LC711" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC712" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">run_interruptible</span><span class="p">(</span><span class="n" style="color: #333;">func</span><span class="p">,</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">args</span><span class="p">,</span> <span class="o" style="font-weight: 600;">**</span><span class="n" style="color: #333;">kwargs</span><span class="p">):</span></span>

</pre>

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713

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713

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<pre style="margin: 0;"> <span id="LC713" class="line" lang="python">    <span class="s" style="color: #d14;">"""Run a function, gracefully handling keyboard interrupts.</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC714" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right">    </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC714" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC715" class="line" lang="python"><span class="s" style="color: #d14;">    Args:</span></span>

</pre>

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<td class="diff-line-num old_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">

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<pre style="margin: 0;"> <span id="LC716" class="line" lang="python"><span class="s" style="color: #d14;">        func: The function to execute.</span></span>

</pre>

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<td class="diff-line-num old_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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<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="s" style="color: #d14;">        args, kwargs: Positional and keyword arguments to pass to `func`.</span></span>

</pre>

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718

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<td class="diff-line-num new_line old" data-linenumber="718" style="width: 35px; color: rgba(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="LC718" 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 old_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">

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<td class="diff-line-num new new_line" data-linenumber="718" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

718

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<pre style="margin: 0;">+<span id="LC718" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="719" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC719" class="line" lang="python"><span class="s" style="color: #d14;">    Returns:</span></span>

</pre>

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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="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">

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<pre style="margin: 0;"> <span id="LC720" class="line" lang="python"><span class="s" style="color: #d14;">        A (unix-style) return code (0=normal, anything else is an error).</span></span>

</pre>

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721

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<td class="diff-line-num new_line old" data-linenumber="721" style="width: 35px; color: rgba(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="LC721" 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 old_line" data-linenumber="722" style="width: 35px; color: rgba(0,0,0,0.3); 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="721" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

721

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<pre style="margin: 0;">+<span id="LC721" class="line" lang="python"></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="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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<pre style="margin: 0;"> <span id="LC722" class="line" lang="python"><span class="s" style="color: #d14;">    Raises:</span></span>

</pre>

</td>

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<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

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

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<pre style="margin: 0;">-<span id="LC723" 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 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">

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<td class="diff-line-num new new_line" data-linenumber="723" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

723

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<pre style="margin: 0;">+<span id="LC723" class="line" lang="python"></span>

</pre>

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<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

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC724" 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="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

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC725" class="line" lang="python">    <span class="n" style="color: #333;">retcode</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="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

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<td class="diff-line-num new_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

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<pre style="margin: 0;"> <span id="LC726" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/atropos/commit/879e6a06365e1352226a649e6d979e1ce87f23f5#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.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">@@ -6,6 +6,7 @@ Cython is run when</td>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="s" style="color: #d14;">* or the pre-generated C sources are out of date,</span></span>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="s" style="color: #d14;">* or when --cython is given on the command line.</span></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">codecs</span></span>

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

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

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

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -24,13 +25,6 @@ if sys.version_info < (3, 3):</td>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python">    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</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="LC26" class="line" lang="python"></span>

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

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span></span>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python">    <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">abspath</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)),</span> <span class="s" style="color: #d14;">"README.md"</span><span class="p">),</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python">    <span class="n" style="color: #333;">encoding</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"utf-8"</span></span>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">f</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC31" 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;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">()</span></span>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">out_of_date</span><span class="p">(</span><span class="n" style="color: #333;">_extensions</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"><span class="s" style="color: #d14;">    Check whether any pyx source is newer than the corresponding generated</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">@@ -145,9 +139,16 @@ setup(</td>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python">    <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"john.didion@nih.gov"</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC140" 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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<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">

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<pre style="margin: 0;"> <span id="LC141" 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="LC142" 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;">codecs</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</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="LC144" class="line" lang="python">            <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">dirname</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">realpath</span><span class="p">(</span><span class="n" style="color: #333;">__file__</span><span class="p">)),</span></span>

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python">            <span class="s" style="color: #d14;">"README.md"</span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python">        <span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python">        <span class="s" style="color: #d14;">"rb"</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python">        <span class="s" style="color: #d14;">"utf-8"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python">    <span class="p">)</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read</span><span class="p">(),</span></span>

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python">    <span class="n" style="color: #333;">long_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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<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;">"<span class="idiff left right">Original Cutadapt code is under MIT license; improvements and additions are in the Public Domain</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); 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="151" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC151" 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;">"<span class="idiff left right">MIT</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC152" 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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<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="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="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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<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">

153

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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">

154

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">    <span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">"bin/atropos"</span><span class="p">],</span></span>

</pre>

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

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="177" style="width: 35px; color: rgba(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">@@ -176,7 +177,6 @@ setup(</td>

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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">

176

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<td class="diff-line-num new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python">        <span class="s" style="color: #d14;">"License :: Public Domain"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

177

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<td class="diff-line-num new_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">

178

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python">        <span class="s" style="color: #d14;">"Natural Language :: English"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num 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">

178

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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">

179

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(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="180" style="width: 35px; color: rgba(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="LC179" class="line" lang="python">        <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.3"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_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">

180

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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="python">        <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.4"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_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">

181

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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">

181

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python">        <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.5"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

182

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<td class="diff-line-num new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC182" class="line" lang="python">        <span class="s" style="color: #d14;">"Programming Language :: Python :: 3.6"</span></span>

</pre>

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