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GitLab

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<h3>

Steffen Möller pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/mcaller/-/commit/6d2245ff0ca9bf95e04aa225fc0a1e14413eb973">6d2245ff</a></strong>

<div>

<span>by Steffen Möller</span>

<i>at 2021-06-19T23:58:58+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upstream does not provide tag for latest changes

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mcaller/-/commit/1d4c1c12b7ae8cc30f37472d8046d6a3b835add2">1d4c1c12</a></strong>

<div>

<span>by Steffen Möller</span>

<i>at 2021-06-19T23:59:32+02:00</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mcaller/-/commit/7a1180cd4801de93cbcc27d82e92abd1e30cbc57">7a1180cd</a></strong>

<div>

<span>by Steffen Möller</span>

<i>at 2021-06-19T23:59:33+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.0.3+git20210331.f7a616a</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mcaller/-/commit/ce5ecfb1e1c3f12ae3ea17a35e2752cfba57ad92">ce5ecfb1</a></strong>

<div>

<span>by Steffen Möller</span>

<i>at 2021-06-19T23:59:47+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.0.3+git20210331.f7a616a'

Update to upstream version '1.0.3+git20210331.f7a616a'

with Debian dir 0bbab8e6783ee0f035b6819bb2a72434ac3b7383</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mcaller/-/commit/20ee86e6cad7216386777daa4da1f0fc87213e96">20ee86e6</a></strong>

<div>

<span>by Steffen Möller</span>

<i>at 2021-06-19T23:59:56+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove unnecessary Team Upload line in changelog.

Changes-By: lintian-brush

</pre>

</li>

</ul>

<h4>19 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

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<li class="file-stats">

<a href="#e50c56a5313a5a9189fe7746adbfd405fca94339">

compare_genomes.py

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<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

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<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">

debian/watch

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<a href="#9924695dba68889deb2c90f7868ec42dae914674">

extract_contexts.py

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<a href="#11b48db4be985feb0b9b1e9c430460f3879bfa68">

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get_positions.py

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<li class="file-stats">

<a href="#09caedf77b7cb38dbbd7c00238109ebc21d5117a">

mCaller.py

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<li class="file-stats">

<a href="#0c8bb5c0c017d1cedf739ded627db6a9f6e7e626">

make_bed.py

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<li class="file-stats">

<a href="#65a2ca2587421e6528362bd4dd0d54c52c8aac02">

testdata/masonread1.eventalign.diffs.6

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testdata/masonread1.methylation.summary.bed

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−

testdata/r95_test_read.eventalign.diffs.6

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testdata/r95_test_read.eventalign.tsv

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testdata/r95_test_read.fast5

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testdata/r95_test_read.fastq

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testdata/r95_test_read.fastq.fast5.fofn

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<a href="#06d66d35a7ff41745fb371e2045cb01d6b459c75">

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testdata/r95_test_read.sam

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<a href="#f4697d3b351cb1b8662ba7fe39d77865b0c5da1a">

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−

testdata/r95_test_read.sorted.bam

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<a href="#a87b5a1e5dc83636a2957fd0c3abeee07d17173a">

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testdata/r95_test_read.sorted.bam.bai

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<a href="#85d3313fac8bf1ae2cd49e275fe72905c0f5ed05">

train_model.py

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<h4>Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

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

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

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

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

7

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">This program is designed to call m6A from nanopore data using the differences between measured and expected currents.  </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

9

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Dependencies/requirements</span></span>

</pre>

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

</td>

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

10

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="gt" style="color: #a00;">> - python3 (as of mCaller version 1.0)</span></span>

</pre>

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

10

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<td class="new_line diff-line-num" 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

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="gt" style="color: #a00;">> - nanopolish (https://github.com/jts/nanopolish)</span></span>

</pre>

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<td class="old_line diff-line-num" 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

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gt" style="color: #a00;">> - an aligner to create a bam file (has been tested with graphmap and bwa mem)</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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

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

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,17 +85,13 @@ arguments:</td>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" 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">

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

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Pipeline for methylation detection from R9 data</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="markdown"><span class="p">1.</span> extract template strand reads from fast5 files<span class="idiff left right"> using a method that saves the file path in the fastq header, eg.</span></span>

</pre>

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<td class="old_line diff-line-num 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">

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<td class="new_line diff-line-num 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">

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="markdown"><span class="p">```</span><span class="nl"><span class="idiff left right"> </span></span></span>

</pre>

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<td class="new_line diff-line-num 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">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="markdown">nanopolish <span class="idiff left">extract -q -t template <fast5 directory> -o</span> <filename>.fastq<span class="idiff right"> </span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="markdown"><span class="p">1.</span> extract template strand reads from fast5 files<span class="idiff left right">. Follow the most up-to-date guidelines from nanopolish (https://github.com/jts/nanopolish). As of April 2019:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC89" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC90" class="line" lang="markdown">nanopolish <span class="idiff left right">index -d <fast5 directory> -s sequencing_summary.txt</span> <filename>.fastq</span>

</pre>

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

</pre>

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

</pre>

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

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="markdown">poretools fastq --type fwd <fast5 directory> > <filename>.fastq </span>

</pre>

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="markdown">  for albacore version > 2.0, follow the most up-to-date guidelines from nanopolish (https://github.com/jts/nanopolish). As of April 2019:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="markdown">nanopolish index -d <fast5 directory> -s sequencing_summary.txt <filename>.fastq</span>

</pre>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="markdown"><span class="p">```</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="markdown"><span class="p">2.</span> align fastq reads to reference assembly (we have used both GraphMap and bwa mem, with comparable results):</span>

</pre>

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="128" style="width: 35px; color: rgba(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="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="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -128,7 +125,7 @@ Results and analysis scripts for the E. coli datasets are provided in the bioRxi</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Test data</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(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="LC131" class="line" lang="markdown">Reference fasta, PacBio calls for m6A and a subset of A positions, and eventalign tsv + fastq are provided for a single read for testing purposes in the "testdata" folder. <span class="idiff left right">The testdata_from_fast5.sh bash script is also included and can be modified with paths to external programs as appropriate to test generation of output from a fast5 file. </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="markdown">Reference fasta, PacBio calls for m6A and a subset of A positions, and eventalign tsv + fastq are provided for a single read for testing purposes in the "testdata" folder. </span>

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="markdown"></span>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="markdown"><span class="p">1.</span> To run mCaller on the testdata, use:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="markdown"><span class="p">```</span><span class="nl"> </span></span>

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<br>

</li>

<li id="e50c56a5313a5a9189fe7746adbfd405fca94339">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#e50c56a5313a5a9189fe7746adbfd405fca94339"><strong>compare_genomes.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">@@ -28,7 +28,8 @@ def compare_by_position(bed1,bed2,xmfa):</td>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">                <span class="n" style="color: #333;">t</span><span class="p">,</span><span class="n" style="color: #333;">pval3</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'none'</span><span class="p">,</span><span class="s" style="color: #d14;">'missing df'</span></span>

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python">            <span class="n" style="color: #333;">d</span><span class="p">,</span><span class="n" style="color: #333;">pval4</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ks_2samp</span><span class="p">(</span><span class="n" style="color: #333;">pos_dict</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">],</span><span class="n" style="color: #333;">pos_dict</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">pos</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="LC30" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pval4</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.9</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">pos_dict</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">pos_dict</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">pval</span><span class="p">,</span> <span class="n" style="color: #333;">pval2</span><span class="p">,</span> <span class="n" style="color: #333;">pval3</span><span class="p">,</span> <span class="n" style="color: #333;">pval4</span></span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">pos_dict</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">pos_dict</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">][</span><span class="n" style="color: #333;">pos</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="n" style="color: #333;">pval</span><span class="p">,</span> <span class="n" style="color: #333;">pval2</span><span class="p">,</span> <span class="n" style="color: #333;">pval3</span><span class="p">,</span> <span class="n" style="color: #333;">pval4</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#print pos, pos_dict[0][pos][0], pos_dict[1][pos][0], pval, pval2, pval3, pval4</span></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="LC34" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC35" 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">@@ -43,7 +44,7 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python">    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

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

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="s" style="color: #d14;">'mCallerNP 0.<span class="idiff right">1'</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="s" style="color: #d14;">'mCallerNP 0.<span class="idiff">3'</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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

</pre>

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49

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">bed1</span><span class="p">),</span> <span class="s" style="color: #d14;">'file not found at '</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;">bed1</span></span>

</pre>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mcaller (1.0.3+git20210331.f7a616a-1) UNRELEASED; urgency=medium</span>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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

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

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Steffen Möller <moeller@debian.org>  Sat, 19 Jun 2021 23:59:32 +0200</span>

</pre>

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

</pre>

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1

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">mcaller (1.0-1) unstable; urgency=medium</span>

</pre>

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2

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

</pre>

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3

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * Initial release (Closes: #969558)</span>

</pre>

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<br>

</li>

<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>

<hr>

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1

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

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>

</pre>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"><span class="idiff left right">#</span>opts="mode=git,pretty=0.3+git%cd.%h" https://github.com/al-mcintyre/mCaller.git HEAD</span>

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%mcaller-$1.tar.gz%" \</span>

</pre>

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4

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<td class="new_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">   https://github.com/al-mcintyre/mCaller/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz</span></pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">opts="mode=git,pretty=<span class="idiff left right">1.</span>0.3+git%cd.%h" https://github.com/al-mcintyre/mCaller.git HEAD</span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"><span class="idiff left right">#</span>opts="filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%mcaller-$1.tar.gz%" \</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"><span class="idiff left right">#</span>   https://github.com/al-mcintyre/mCaller/tags (?:.*?/)?v?(\d[\d.]*)\.tar\.gz</span></pre>

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<br>

</li>

<li id="9924695dba68889deb2c90f7868ec42dae914674">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#9924695dba68889deb2c90f7868ec42dae914674"><strong>extract_contexts.py</strong></a>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,8 +2,8 @@ from collections import defaultdict</td>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scipy.stats</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ss</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">cPickle</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>import _pickle as cPickle</span></span>

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

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>import cPickle</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;"><span class="idiff left">pickle</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#</span>_pickle as cPickle</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">re</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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;">os</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -121,7 +121,7 @@ def extract_features(tsv_input,fasta_input,read2qual,k,skip_thresh,qual_thresh,m</td>

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<pre style="margin: 0;"> <span id="LC121" 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;">train</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="python">        <span class="n" style="color: #333;">tsv_output</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'.'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">tsv_input</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[:</span><span class="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="s" style="color: #d14;">'.diffs.'</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;">k</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.tmp'</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;">startline</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">        <span class="n" style="color: #333;">modfi</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">modelfile</span><span class="p">,</span><span class="s" style="color: #d14;">'rb'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python">        <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">cP</span>ickle</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">modfi</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="python">        <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">p</span>ickle</span><span class="p">.</span><span class="n" style="color: #333;">load</span><span class="p">(</span><span class="n" style="color: #333;">modfi</span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">encoding</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'latin'</span></span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">        <span class="n" style="color: #333;">modfi</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">type</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python">            <span class="n" style="color: #333;">model</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'general'</span><span class="p">:</span><span class="n" style="color: #333;">model</span><span class="p">}</span> <span class="c1" style="color: #998; font-style: italic;">#for compatibility with previously trained model</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -139,11 +139,18 @@ def extract_features(tsv_input,fasta_input,read2qual,k,skip_thresh,qual_thresh,m</td>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#tsv format: ecoli   805 CGCCAT  cc1da58e-3db3-4a4b-93c2-c78e1dbe6aba:1D_000:template    t   1   102.16  0.963   0.00175 CGCCAT  102.23  1.93    -0.03   101.973,100.037,102.403,101.758,104.338,102.618,101.973</span></span>

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">tsv_input</span><span class="p">,</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">tsv</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;">tsv</span><span class="p">.</span><span class="n" style="color: #333;">seek</span><span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">startline</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">500</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="LC142" class="line" lang="python">        <span class="n" style="color: #333;">tsv</span><span class="p">.</span><span class="n" style="color: #333;">readline</span><span class="p">()</span> <span class="c1" style="color: #998; font-style: italic;">#to start new line</span></span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">tsv</span><span class="p">.</span><span class="n" style="color: #333;">tell</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">endline</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">500</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">#TODO: why 500? </span></span>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="python">            <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tsv</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">(</span><span class="mi" style="color: #099;">8000000</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#TODO: why 8M? </span></span>

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python">        <span class="n" style="color: #333;">linepos</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;">startline</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">500</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="LC143" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#startline, endline, and linepos are in characters -- previously used tsv.tell(), but incompatible with python3</span></span>

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python">        <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">linepos</span> <span class="o" style="font-weight: 600;"><=</span> <span class="n" style="color: #333;">endline</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">500</span><span class="p">:</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;">#print('current position',linepos)</span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python">            <span class="n" style="color: #333;">lines</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tsv</span><span class="p">.</span><span class="n" style="color: #333;">readlines</span><span class="p">(</span><span class="mi" style="color: #099;">8000000</span><span class="p">)</span> <span class="c1" style="color: #998; font-style: italic;">#TODO: why 8M? reasonable size for memory consumption, but could change</span></span>

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

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python">                <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">read_pos</span><span class="p">,</span> <span class="n" style="color: #333;">read_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">read_ind</span><span class="p">,</span> <span class="n" style="color: #333;">event_current</span><span class="p">,</span> <span class="n" style="color: #333;">event_sd</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">ref_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">model_current</span><span class="p">,</span> <span class="n" style="color: #333;">ref_sd</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[:</span><span class="mi" style="color: #099;">12</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;">linepos</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;">line</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python">                <span class="k" style="font-weight: 600;">try</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;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">read_pos</span><span class="p">,</span> <span class="n" style="color: #333;">read_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">read_name</span><span class="p">,</span> <span class="n" style="color: #333;">x</span><span class="p">,</span> <span class="n" style="color: #333;">read_ind</span><span class="p">,</span> <span class="n" style="color: #333;">event_current</span><span class="p">,</span> <span class="n" style="color: #333;">event_sd</span><span class="p">,</span> <span class="n" style="color: #333;">y</span><span class="p">,</span> <span class="n" style="color: #333;">ref_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">model_current</span><span class="p">,</span> <span class="n" style="color: #333;">ref_sd</span>  <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">()[:</span><span class="mi" style="color: #099;">12</span><span class="p">]</span></span>

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python">                <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python">                    <span class="k" style="font-weight: 600;">continue</span></span>

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

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<pre style="margin: 0;"> <span id="LC154" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">chrom</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">last_contig</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python">                    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">                        <span class="n" style="color: #333;">meth_fwd</span><span class="p">,</span><span class="n" style="color: #333;">meth_rev</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">find_and_methylate</span><span class="p">(</span><span class="n" style="color: #333;">fasta_input</span><span class="p">,</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span><span class="n" style="color: #333;">base</span><span class="p">,</span><span class="n" style="color: #333;">motif</span><span class="p">,</span><span class="n" style="color: #333;">positions_list</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -167,9 +174,6 @@ def extract_features(tsv_input,fasta_input,read2qual,k,skip_thresh,qual_thresh,m</td>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python">                    <span class="n" style="color: #333;">meth_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">meth_rev</span></span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python">                <span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">read_pos</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python">                <span class="n" style="color: #333;">reference_kmer</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">meth_ref</span><span class="p">[</span><span class="n" style="color: #333;">read_pos</span><span class="p">:</span><span class="n" style="color: #333;">read_pos</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">k</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#if read_name == last_read and (reference_kmer != revcomp('M'.join(ref_kmer.split('A')),rev) and reference_kmer != revcomp('M'.join(ref_kmer.split('T')),rev)) : #true at pseudomethylated positions (to check) TODO: remove this</span></span>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#    print 'issue with reference kmer in line', line, reference_kmer, rev, revcomp('M'.join(ref_kmer.split('A')),rev)</span></span>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="python">                <span class="c1" style="color: #998; font-style: italic;">#    sys.exit(0)</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="c1" style="color: #998; font-style: italic;">#if finished context for previous potentially modified position, save and reset</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mpos</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">((</span><span class="n" style="color: #333;">read_pos</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">mpos</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">read_name</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">last_read</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">read_name</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">last_read</span><span class="p">)):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -212,15 +216,15 @@ def extract_features(tsv_input,fasta_input,read2qual,k,skip_thresh,qual_thresh,m</td>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python">                                <span class="n" style="color: #333;">towrite</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">chrom</span><span class="p">,</span><span class="n" style="color: #333;">last_read</span><span class="p">,</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">mpos</span><span class="p">),</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">diff</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">diff</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">diffs</span><span class="p">]),</span><span class="n" style="color: #333;">strand</span><span class="p">(</span><span class="n" style="color: #333;">last_rev</span><span class="p">),</span><span class="n" style="color: #333;">label</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python">                                <span class="n" style="color: #333;">last_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last_read</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</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;">mpos</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">diff</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">diff</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">diffs</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strand</span><span class="p">(</span><span class="n" style="color: #333;">last_rev</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="python">                            <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">IndexError</span><span class="p">,</span><span class="nb" style="color: #0086b3;">KeyError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">last_read</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</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;">mpos</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">diff</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">diff</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">diffs</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strand</span><span class="p">(</span><span class="n" style="color: #333;">last_rev</span><span class="p">),</span><span class="s" style="color: #d14;">'- Index or Key Error'</span></span>

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<pre style="margin: 0;">-<span id="LC216" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">(),</span> <span class="n" style="color: #333;">base_model</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">(),</span> <span class="n" style="color: #333;">context</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">context</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">context</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="mi" style="color: #099;">2</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC217" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="n" style="color: #333;"><span class="idiff right">e</span></span></span>

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<pre style="margin: 0;">-<span id="LC218" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">model</span><span class="p">[</span><span class="n" style="color: #333;">twobase_model</span><span class="p">].</span><span class="n" style="color: #333;">predict_proba</span><span class="p">([</span><span class="n" style="color: #333;">diffs</span><span class="p">])</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC219" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">last_read</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</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;">mpos</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">diff</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">diff</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">diffs</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strand</span><span class="p">(</span><span class="n" style="color: #333;">last_rev</span><span class="p">),</span><span class="s" style="color: #d14;">'- Index or Key Error'</span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC220" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">model</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">(),</span> <span class="n" style="color: #333;">base_model</span><span class="p">.</span><span class="n" style="color: #333;">keys</span><span class="p">(),</span> <span class="n" style="color: #333;">context</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">context</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="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">context</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="mi" style="color: #099;">2</span><span class="p">]<span class="idiff right">)</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC221" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;"><span class="idiff">e</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC222" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">model</span><span class="p">[</span><span class="n" style="color: #333;">twobase_model</span><span class="p">].</span><span class="n" style="color: #333;">predict_proba</span><span class="p">([</span><span class="n" style="color: #333;">diffs</span><span class="p">])<span class="idiff right">)</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python">                                <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</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="LC224" class="line" lang="python">                        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="python">                            <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">last_read</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</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;">mpos</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">diff</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">diff</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">diffs</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strand</span><span class="p">(</span><span class="n" style="color: #333;">last_rev</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="225" style="width: 35px; color: rgba(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="LC222" class="line" lang="python">                            <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">read_name</span><span class="p">,</span> <span class="n" style="color: #333;">rev</span><span class="p">,</span> <span class="n" style="color: #333;">last_read</span><span class="p">,</span> <span class="n" style="color: #333;">last_rev</span><span class="p">,</span> <span class="n" style="color: #333;">last_first</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="225" style="width: 35px; color: rgba(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="LC223" class="line" lang="python">                            <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">read_kmer</span><span class="p">,</span><span class="n" style="color: #333;">reference_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">ref_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">last_pos_in_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">mspacing</span><span class="p">,</span> <span class="n" style="color: #333;">pos_in_kmer</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python">                            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">last_read</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</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;">mpos</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">context</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">diff</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">diff</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">diffs</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">strand</span><span class="p">(</span><span class="n" style="color: #333;">last_rev</span><span class="p">)<span class="idiff right">)</span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="python">                            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">read_name</span><span class="p">,</span> <span class="n" style="color: #333;">rev</span><span class="p">,</span> <span class="n" style="color: #333;">last_read</span><span class="p">,</span> <span class="n" style="color: #333;">last_rev</span><span class="p">,</span> <span class="n" style="color: #333;">last_first</span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="python">                            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">read_kmer</span><span class="p">,</span><span class="n" style="color: #333;">reference_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">ref_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">last_pos_in_kmer</span><span class="p">,</span> <span class="n" style="color: #333;">mspacing</span><span class="p">,</span> <span class="n" style="color: #333;">pos_in_kmer</span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python">                            <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</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="LC229" class="line" lang="python">                        <span class="n" style="color: #333;">num_observations</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="LC230" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">num_observations</span><span class="o" style="font-weight: 600;">%</span><span class="mi" style="color: #099;">5000</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 unfold js-unfold 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">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -252,12 +256,12 @@ def extract_features(tsv_input,fasta_input,read2qual,k,skip_thresh,qual_thresh,m</td>

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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python">                        <span class="n" style="color: #333;">diff_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">diffs</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python">                        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">diff_col</span><span class="p">)</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">k</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python">                            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">last_info</span><span class="p">,</span><span class="s" style="color: #d14;">'- n diffs off'</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC259" class="line" lang="python">                                <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">last_info</span><span class="p">,</span><span class="s" style="color: #d14;">'- n diffs off'</span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python">                            <span class="k" style="font-weight: 600;">except</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python">                                <span class="k" style="font-weight: 600;">pass</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python">                            <span class="c1" style="color: #998; font-style: italic;">#GGCGCM 613883 613878 False 2289b392-746e-4fa0-8226-d3ac661c9620_Basecall_2D_template 2289b392-746e-4fa0-8226-d3ac661c9620_Basecall_2D_template [[], [], [], [], [], [], []] 7</span></span>

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="264" style="width: 35px; color: rgba(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="LC260" class="line" lang="python">                            <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">reference_kmer</span><span class="p">,</span><span class="n" style="color: #333;">last_mpos</span><span class="p">,</span><span class="n" style="color: #333;">mpos</span><span class="p">,</span><span class="n" style="color: #333;">mspacing</span><span class="p">,</span><span class="n" style="color: #333;">read_pos</span><span class="p">,</span><span class="n" style="color: #333;">read_pos</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">last_mpos</span><span class="p">,</span><span class="n" style="color: #333;">read_name</span><span class="p">,</span><span class="n" style="color: #333;">last_read</span><span class="p">,</span><span class="n" style="color: #333;">diff_col</span><span class="p">,</span><span class="n" style="color: #333;">mspacing</span><span class="p">,</span> <span class="n" style="color: #333;">last_diff_col</span><span class="p">,</span> <span class="n" style="color: #333;">last_diff_col</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mspacing</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC264" class="line" lang="python">                            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">reference_kmer</span><span class="p">,</span><span class="n" style="color: #333;">last_mpos</span><span class="p">,</span><span class="n" style="color: #333;">mpos</span><span class="p">,</span><span class="n" style="color: #333;">mspacing</span><span class="p">,</span><span class="n" style="color: #333;">read_pos</span><span class="p">,</span><span class="n" style="color: #333;">read_pos</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">last_mpos</span><span class="p">,</span><span class="n" style="color: #333;">read_name</span><span class="p">,</span><span class="n" style="color: #333;">last_read</span><span class="p">,</span><span class="n" style="color: #333;">diff_col</span><span class="p">,</span><span class="n" style="color: #333;">mspacing</span><span class="p">,</span> <span class="n" style="color: #333;">last_diff_col</span><span class="p">,</span> <span class="n" style="color: #333;">last_diff_col</span><span class="p">[:</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">mspacing</span><span class="p">]<span class="idiff right">)</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC265" class="line" lang="python">                            <span class="n" style="color: #333;">diff_col</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[[]</span> <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;">k</span><span class="p">)]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python">                            <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"></span>

</pre>

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<br>

</li>

<li id="11b48db4be985feb0b9b1e9c430460f3879bfa68">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#11b48db4be985feb0b9b1e9c430460f3879bfa68"><strong>get_positions.py</strong></a>

<hr>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">Bio</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">SeqIO</span></span>

</pre>

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scipy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">stats</span></span>

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">scipy.cluster.hierarchy</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">fcluster</span><span class="p">,</span><span class="n" style="color: #333;">linkage</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">scipy.spatial.distance</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">ssd</span></span>

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">extract_contexts</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">revcomp</span></span>

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

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plotlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">plot_w_labels</span></span>

</pre>

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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</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pandas</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">pd</span></span>

</pre>

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

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

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_pos_set</span><span class="p">(</span><span class="n" style="color: #333;">pos_list</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python">    <span class="n" style="color: #333;">pos_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python">    <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">pos_list</span><span class="p">,</span><span class="s" style="color: #d14;">'r'</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fi</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">fi</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">)</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">3</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python">                <span class="n" style="color: #333;">pos_set</span><span class="p">.</span><span class="n" style="color: #333;">add</span><span class="p">(</span><span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">().</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">)[:</span><span class="mi" style="color: #099;">4</span><span class="p">]))</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">pos_set</span></span>

</pre>

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

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">aggregate_by_pos</span><span class="p">(</span><span class="n" style="color: #333;">meth_fi</span><span class="p">,</span><span class="n" style="color: #333;">aggfi</span><span class="p">,</span><span class="n" style="color: #333;">depth_thresh</span><span class="p">,</span><span class="n" style="color: #333;">mod_thresh</span><span class="p">,</span><span class="n" style="color: #333;">pos_list</span><span class="p">,</span><span class="n" style="color: #333;">control</span><span class="p">,</span><span class="n" style="color: #333;">verbose_results</span><span class="p">,</span><span class="n" style="color: #333;">gff</span><span class="p">,</span><span class="n" style="color: #333;">ref</span><span class="p">,</span><span class="n" style="color: #333;">plot</span><span class="p">,</span><span class="n" style="color: #333;">plotdir</span><span class="p">,</span><span class="n" style="color: #333;">plotsummary</span><span class="p">):</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">    <span class="n" style="color: #333;">pos_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose_results</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python">        <span class="n" style="color: #333;">pos_dict_verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos_list</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">        <span class="n" style="color: #333;">pos_set</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">make_pos_set</span><span class="p">(</span><span class="n" style="color: #333;">pos_list</span><span class="p">)</span></span>

</pre>

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

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

</pre>

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

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python">    <span class="n" style="color: #333;">values_dict</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">meth_fi</span><span class="p">,</span><span class="s" style="color: #d14;">'r'</span><span class="p">):</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#try:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;">#print line</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python">            <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">                <span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">read</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">values</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">,</span><span class="n" style="color: #333;">label</span><span class="p">,</span><span class="n" style="color: #333;">prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">))</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="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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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">#for backwards compatibility; does not work with verbose results</span></span>

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

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python">                <span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">read</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">values</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">,</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python">            <span class="n" style="color: #333;">nextpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</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="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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

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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="n" style="color: #333;">pos_list</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pos_set</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pos_dict</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC41" class="line" lang="python">                <span class="n" style="color: #333;">pos_dict</span><span class="p">[(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC42" class="line" lang="python">                <span class="n" style="color: #333;">values_dict</span><span class="p">[(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="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="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">verbose_results</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" 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 class="n" style="color: #333;">pos_dict_verbose</span><span class="p">[(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="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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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos_list</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pos_set</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">pos_list</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">plot</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python">                <span class="n" style="color: #333;">values_dict</span><span class="p">[(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)].</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">v</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">v</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">values</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">','</span><span class="p">)][:</span><span class="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="LC47" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">label</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'m'</span><span class="p">:</span></span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python">                <span class="n" style="color: #333;">pos_dict</span><span class="p">[(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)].</span><span class="n" style="color: #333;">append</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="LC49" 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="LC50" class="line" lang="python">                <span class="n" style="color: #333;">pos_dict</span><span class="p">[(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)].</span><span class="n" style="color: #333;">append</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="LC51" class="line" lang="python"></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#parse command line options</span></span>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">argparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">ArgumentParser</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python">    <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">ArgumentParser</span><span class="p">(</span><span class="n" style="color: #333;">description</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Produce bed file of methylated positions based on mCaller output'</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-d'</span><span class="p">,</span><span class="s" style="color: #d14;">'--min_read_depth'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'minimum coverage of position to determine methylation (default = 15)'</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;">15</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-t'</span><span class="p">,</span><span class="s" style="color: #d14;">'--mod_threshold'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">float</span><span class="p">,</span><span class="n" style="color: #333;">required</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">False</span><span class="p">,</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'minimum %% of observations at a position to include in report (default = 0.5)'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mf" style="color: #099;">0.5</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-f'</span><span class="p">,</span><span class="s" style="color: #d14;">'--mCaller_file'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'the output file from mCaller to summarize'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-p'</span><span class="p">,</span><span class="s" style="color: #d14;">'--positions'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'~bed file of positions for which to calculate % methylated (chromosome,start,end,strand); ignores other thresholds'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--control'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'take unmethylated positions as a control for motif detection'</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC61" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--gff'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'output PacBio-style gff instead of bed ("identificationQv" score will be average probability of methylation)'</span><span class="p">)</span></span>

</pre>

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</td>

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

62

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--ref'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'use reference fasta to output longer contexts surrounding a base, from -20 to +20'</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--plot'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'plot currents deviations at the positions included (not recommended for many positions)'</span><span class="p">)</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--plotsummary'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'plot currents deviations summarized across the positions included'</span><span class="p">)</span></span>

</pre>

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

</td>

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

65

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--plotdir'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'mCaller_position_plots'</span><span class="p">,</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'output directory for plots, default=mCaller_position_plots'</span><span class="p">)</span></span>

</pre>

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</td>

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

66

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--vo'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'verbose output including probabilities for each position'</span><span class="p">)</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

67

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'print version'</span><span class="p">)</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

68

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python">    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

69

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

<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

70

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

<pre style="margin: 0;">+<span id="LC70" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">:</span></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

71

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

<pre style="margin: 0;">+<span id="LC71" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'mCallerNP 0.3'</span></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

72

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

<pre style="margin: 0;">+<span id="LC72" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

73

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

<pre style="margin: 0;">+<span id="LC73" class="line" lang="python"></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mCaller_file</span><span class="p">),</span> <span class="s" style="color: #d14;">'file not found at '</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;">mCaller_file</span></span>

</pre>

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</td>

<td class="new_line diff-line-num new" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

75

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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;">args</span><span class="p">.</span><span class="n" style="color: #333;">positions</span><span class="p">:</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

76

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">        <span class="n" style="color: #333;">output_file</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;">mCaller_file</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.methylation.positions.summary'</span></span>

</pre>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

77

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">control</span><span class="p">:</span></span>

</pre>

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</td>

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

78

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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="python">        <span class="n" style="color: #333;">output_file</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;">mCaller_file</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.methylation.summary'</span></span>

</pre>

</td>

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

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<td class="new_line diff-line-num new" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

79

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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</td>

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

80

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="python">        <span class="n" style="color: #333;">output_file</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;">mCaller_file</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.methylation.control.summary'</span></span>

</pre>

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

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

81

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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="LC81" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gff</span><span class="p">:</span></span>

</pre>

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

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<td class="new_line diff-line-num new" 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="python">        <span class="n" style="color: #333;">output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_file</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.gff'</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

83

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

</td>

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

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<td class="new_line diff-line-num new" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

84

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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="LC84" class="line" lang="python">        <span class="n" style="color: #333;">output_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">output_file</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.bed'</span></span>

</pre>

</td>

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

</td>

<td class="new_line diff-line-num new" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

85

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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="LC85" 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;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotdir</span><span class="p">):</span></span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

86

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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="LC86" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotdir</span><span class="p">)</span></span>

</pre>

</td>

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

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

87

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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="LC87" class="line" lang="python"></span>

</pre>

</td>

</tr>

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

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<td class="new_line diff-line-num new" 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="python">    <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mCaller_file</span></span>

</pre>

</td>

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

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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

89

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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="LC89" class="line" lang="python"></span>

</pre>

</td>

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

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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

90

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="python">    <span class="n" style="color: #333;">aggregate_by_pos</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mCaller_file</span><span class="p">,</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_read_depth</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mod_threshold</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">positions</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">control</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">vo</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gff</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">ref</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotdir</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotsummary</span><span class="p">)</span></span>

</pre>

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

91

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

</pre>

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<td class="new_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"__main__"</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC93" class="line" lang="python">    <span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>

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<br>

</li>

<li id="09caedf77b7cb38dbbd7c00238109ebc21d5117a">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#09caedf77b7cb38dbbd7c00238109ebc21d5117a"><strong>mCaller.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">@@ -3,9 +3,8 @@</td>

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3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#Alexa McIntyre, 2016-2018</span></span>

</pre>

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4

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

</pre>

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

5

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

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

6

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span> <span class="o" style="font-weight: 600;">>=</span> <span class="p">(</span><span class="mi" style="color: #099;">2</span><span class="p">,</span><span class="mi" style="color: #099;">7</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="s" style="color: #d14;">'please use python 2.7'</span></span>

</pre>

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7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">cPickle</span></span>

</pre>

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8

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

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#import _pickle as cPickle</span></span>

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="python"><span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">version_info</span> <span class="o" style="font-weight: 600;">>=</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span><span class="mi" style="color: #099;">0</span><span class="p">),</span> <span class="s" style="color: #d14;">'please use python3'</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pickle</span> </span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">defaultdict</span></span>

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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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;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#import time</span></span>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -138,7 +137,7 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-c'</span><span class="p">,</span><span class="s" style="color: #d14;">'--classifier'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'use alternative classifier: options = NN (default), RF, LR, or NBC (non-default may significantly increase runtime)'</span><span class="p">,</span><span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'NN'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--plot_training'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'plot probabilities distributions for training positions (requires labels in positions file and --train)'</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;">False</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#parser.add_argument('--plot_violin',action='store_true',required=False,help='train a new model (requires labels in positions file)',default=False)</span></span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'version'</span><span class="p">,</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'print version'</span><span class="p">,</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'%(prog)s v<span class="idiff left right">0.3</span>'</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;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'version'</span><span class="p">,</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'print version'</span><span class="p">,</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'%(prog)s v<span class="idiff left right">1.0</span>'</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;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</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;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">base</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'A'</span><span class="p">:</span></span>

</pre>

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<br>

</li>

<li id="0c8bb5c0c017d1cedf739ded627db6a9f6e7e626">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#0c8bb5c0c017d1cedf739ded627db6a9f6e7e626"><strong>make_bed.py</strong></a>

<hr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -81,7 +81,7 @@ def aggregate_by_pos(meth_fi,aggfi,depth_thresh,mod_thresh,pos_list,control,verb</td>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span><span class="p">:</span> <span class="c1" style="color: #998; font-style: italic;">#for backwards compatibility; does not work with verbose results</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">                <span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">read</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">values</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">,</span><span class="n" style="color: #333;">label</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">tuple</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">            <span class="n" style="color: #333;">nextpos</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</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="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos_list</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pos_set</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">context</span><span class="p">[</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">context</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="s" style="color: #d14;">'M'</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">pos_list</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pos_set</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">context</span><span class="p">[</span><span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">context</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 class="idiff right">)</span>]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">'M'</span><span class="p">):</span></span>

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<td class="old_line diff-line-num" 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">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">pos_dict</span><span class="p">:</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">                <span class="n" style="color: #333;">pos_dict</span><span class="p">[(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,6 +98,7 @@ def aggregate_by_pos(meth_fi,aggfi,depth_thresh,mod_thresh,pos_list,control,verb</td>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python">                <span class="n" style="color: #333;">pos_dict_verbose</span><span class="p">[(</span><span class="n" style="color: #333;">csome</span><span class="p">,</span><span class="n" style="color: #333;">pos</span><span class="p">,</span><span class="n" style="color: #333;">nextpos</span><span class="p">,</span><span class="n" style="color: #333;">context</span><span class="p">,</span><span class="n" style="color: #333;">strand</span><span class="p">)].</span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">prob</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">())</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#except:</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;">#    pass</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC101" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">values_dict</span><span class="p">)</span></span>

</pre>

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

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<td class="new_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">plotsummary</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">'plotting all current deviations...'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python">        <span class="n" style="color: #333;">num2lab</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="s" style="color: #d14;">'A'</span><span class="p">,</span><span class="mi" style="color: #099;">1</span><span class="p">:</span><span class="s" style="color: #d14;">'m6A'</span><span class="p">}</span></span>

</pre>

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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>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -149,6 +150,7 @@ def aggregate_by_pos(meth_fi,aggfi,depth_thresh,mod_thresh,pos_list,control,verb</td>

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<td class="new_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC150" class="line" lang="python">                <span class="n" style="color: #333;">gff_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">locus</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span><span class="n" style="color: #333;">locus</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">],</span><span class="n" style="color: #333;">locus</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">],</span><span class="n" style="color: #333;">deets</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="new_line diff-line-num" 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="python">                <span class="n" style="color: #333;">write_gff</span><span class="p">(</span><span class="n" style="color: #333;">outfi</span><span class="p">,</span><span class="n" style="color: #333;">gff_info</span><span class="p">)</span></span>

</pre>

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

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<td class="new_line diff-line-num" 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="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC153" class="line" lang="python">                <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="n" style="color: #333;">aggfi</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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="LC154" class="line" lang="python">                <span class="n" style="color: #333;">out_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">locus</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="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">np</span><span class="p">.</span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">pos_dict</span><span class="p">[</span><span class="n" style="color: #333;">locus</span><span class="p">]))]</span><span class="o" style="font-weight: 600;">+</span><span class="p">[</span><span class="n" style="color: #333;">locus</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="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">pos_dict</span><span class="p">[</span><span class="n" style="color: #333;">locus</span><span class="p">]))])</span> <span class="c1" style="color: #998; font-style: italic;">#+[str(x) for x in values_dict[locus]])</span></span>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos_list</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">                    <span class="n" style="color: #333;">out_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">out_line</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">'</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">values_dict</span><span class="p">[</span><span class="n" style="color: #333;">locus</span><span class="p">]])</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -157,9 +159,9 @@ def aggregate_by_pos(meth_fi,aggfi,depth_thresh,mod_thresh,pos_list,control,verb</td>

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<pre style="margin: 0;"> <span id="LC159" class="line" lang="python">                <span class="n" style="color: #333;">outfi</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="n" style="color: #333;">out_line</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">'</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC160" 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;">pos_list</span><span class="p">:</span></span>

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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="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">control</span><span class="p">:</span></span>

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<td class="new_line diff-line-num old" data-linenumber="162" style="width: 35px; color: rgba(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="LC160" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="s" style="color: #d14;">'methylated loci found with min depth'</span><span class="p">,</span> <span class="n" style="color: #333;">depth_thresh</span><span class="p">,</span> <span class="s" style="color: #d14;">'reads'</span></span>

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<pre style="margin: 0;">+<span id="LC162" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="s" style="color: #d14;">'methylated loci found with min depth'</span><span class="p">,</span> <span class="n" style="color: #333;">depth_thresh</span><span class="p">,</span> <span class="s" style="color: #d14;">'reads'</span><span class="p"><span class="idiff right">)</span></span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="python">        <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="new_line diff-line-num old" data-linenumber="164" style="width: 35px; color: rgba(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="LC162" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="s" style="color: #d14;">'unmethylated loci found with min depth'</span><span class="p">,</span> <span class="n" style="color: #333;">depth_thresh</span><span class="p">,</span> <span class="s" style="color: #d14;">'reads'</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC164" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">count</span><span class="p">,</span> <span class="s" style="color: #d14;">'unmethylated loci found with min depth'</span><span class="p">,</span> <span class="n" style="color: #333;">depth_thresh</span><span class="p">,</span> <span class="s" style="color: #d14;">'reads'</span><span class="p"><span class="idiff right">)</span></span></span>

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

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;">#parse command line options</span></span>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -176,13 +178,9 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--plotsummary'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'plot currents deviations summarized across the positions included'</span><span class="p">)</span></span>

</pre>

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177

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--plotdir'</span><span class="p">,</span><span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'mCaller_position_plots'</span><span class="p">,</span><span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'output directory for plots, default=mCaller_position_plots'</span><span class="p">)</span></span>

</pre>

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178

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<td class="new_line diff-line-num" 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;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--vo'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span><span class="n" style="color: #333;">required</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;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'verbose output including probabilities for each position'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="181" style="width: 35px; color: rgba(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="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left">store_true'</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">required</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="bp" style="color: #999;"><span class="idiff">False</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">help</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'print version</span>'</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="181" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC181" class="line" lang="python">    <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span><span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'<span class="idiff left">version'</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">help</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff">'print version'</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">version</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s" style="color: #d14;"><span class="idiff right">'%(prog)s v1.0</span>'</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python">    <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">parse_args</span><span class="p">()</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="old_line diff-line-num old" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="new_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(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="LC182" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">version</span><span class="p">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(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="LC183" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">'mCallerNP 0.3'</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(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="LC184" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="184" style="width: 35px; color: rgba(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="LC185" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" 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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<td class="new_line diff-line-num" 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="python">    <span class="k" style="font-weight: 600;">assert</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mCaller_file</span><span class="p">),</span> <span class="s" style="color: #d14;">'file not found at '</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;">mCaller_file</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">positions</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python">        <span class="n" style="color: #333;">output_file</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;">mCaller_file</span><span class="p">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">)[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">'.methylation.positions.summary'</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="197" style="width: 35px; color: rgba(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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -197,7 +195,7 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC195" 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;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotdir</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

198

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<td class="new_line diff-line-num" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">mkdir</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotdir</span><span class="p">)</span></span>

</pre>

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199

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<td class="new_line diff-line-num" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

197

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="python"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mCaller_file</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC198" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mCaller_file</span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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

201

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<td class="new_line diff-line-num" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

199

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

</pre>

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<td class="old_line diff-line-num" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

202

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<td class="new_line diff-line-num" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="python">    <span class="n" style="color: #333;">aggregate_by_pos</span><span class="p">(</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mCaller_file</span><span class="p">,</span><span class="n" style="color: #333;">output_file</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">min_read_depth</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">mod_threshold</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">positions</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">control</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">vo</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">gff</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">ref</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plot</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotdir</span><span class="p">,</span><span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">plotsummary</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

203

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

201

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

</pre>

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<br>

</li>

<li id="65a2ca2587421e6528362bd4dd0d54c52c8aac02">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#65a2ca2587421e6528362bd4dd0d54c52c8aac02"><strong>testdata/masonread1.eventalign.diffs.6</strong></a>

<hr>

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1

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

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template     13673   CATTAMCAATC     1.1,-0.236666666667,0.28,1.17,-0.02,0.67,7.05526534938  -       A</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template     13861   GCCCGMTATAT     -0.53,-2.56,-0.46,-2.09,-5.4,1.05,7.05526534938 -       A</span>

</pre>

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<td class="old_line diff-line-num 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">

3

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

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template     14331   TTTTGMGATCC     0.06,-1.6,-3.48,1.365,1.06,3.94,7.05526534938   -       m6A</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template     14352   TCGTGMATGCA     2.98,1.47,-2.14,5.63,1.07,5.135,7.05526534938   -       A</span>

</pre>

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

5

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template     14444   TAAAAMAGAGA     -0.68,-0.74,-0.585,-0.48,-0.815,-1.08,7.05526534938     -       A</span>

</pre>

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

6

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template     14528   ATCAAMCCGAG     4.025,-0.115,-1.02,-0.48,0.173333333333,1.19,7.05526534938      -       A</span>

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7

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template     14836   GCTTTMGCAAA     -1.37333333333,0.18,-0.613333333333,-1.43,-0.005,-4.32,7.05526534938    -       A</span>

</pre>

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<td class="old_line diff-line-num 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">

8

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

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template     15536   TGCGTMTTCAA     -0.1,2.23,-2.058,2.78,-0.68,0.51,7.05526534938  -       m6A</span>

</pre>

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

9

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

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template     15630   CTTCCMGCCAC     -2.72,-1.03,-0.14,2.625,1.0375,-1.075,7.05526534938     -       A</span>

</pre>

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10

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

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    16154   AGATAMTAAAT     -2.38,-1.03,-2.88333333333,-0.59,-4.31,-4.94,7.05526534938      -       A</span>

</pre>

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<td class="old_line diff-line-num 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">

11

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    16209   TCTTAMTAACA     -0.3075,4.23,0.88,0.326666666667,-4.165,0.93,7.05526534938      -       A</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    16397   GTATTMTCAAT     -0.63,-2.97,-0.736666666667,-2.71,-1.12,-3.25111111111,7.05526534938    -       A</span>

</pre>

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<td class="old_line diff-line-num 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">

13

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

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    16979   AAATGMGATTT     -1.44,-5.03,1.445,0.4,-0.588,-0.55,7.05526534938        -       A</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

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

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    17243   AGTAGMTTGAT     -1.44333333333,-0.02,-0.0366666666667,-0.55,0.64,-2.71,7.05526534938    -       A</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

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

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    17283   ACTTAMCCGGT     -1.23,-1.635,-0.24,1.10333333333,-2.215,-2.93,7.05526534938     -       A</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

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

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    17486   AGCATMTTTAT     -0.21,0.075,-1.30833333333,4.15,-0.3,-0.215,7.05526534938       -       A</span>

</pre>

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<td class="old_line diff-line-num 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">

17

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

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    17796   GTTATMTGCAA     -1.355,-0.34,-1.86333333333,-1.87,-1.265,-1.22,7.05526534938    -       A</span>

</pre>

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<td class="old_line diff-line-num 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">

18

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

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    17923   GGTAAMAATTT     -5.64,-3.6,-5.13,-0.255,0.4,0.73,7.05526534938  -       A</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

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

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    18402   GTGACMGTTTT     -1.14,0.94,-4.55,2.0,-0.34,-2.71,7.05526534938  -       m6A</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

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

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    18488   GGCTTMTTTTA     1.02,-2.38,0.915,0.05,1.75,0.8875,7.05526534938 -       A</span>

</pre>

</td>

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<td class="old_line diff-line-num 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">

21

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

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    18575   GGATGMAAGAA     -0.56,-3.505,1.02,-1.55,-0.714,-0.4825,7.05526534938    -       A</span>

</pre>

</td>

</tr>

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<td class="old_line diff-line-num 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">

22

</td>

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

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    18804   ATATTMTGCAT     3.49,1.3,-1.495,-2.3,-1.2,-0.62,7.05526534938   -       A</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

23

</td>

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

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    18828   TCGTGMAAAAT     -1.405,-2.96,-3.1,0.57,-0.433333333333,-1.44,7.05526534938      -       A</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

24

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

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    20255   AGGCCMTTCAA     -2.15,1.885,2.58,-0.36,4.26,-2.4625,7.05526534938       -       m6A</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

25

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

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    20591   AATCAMAAGAA     1.485,4.095,-1.12,-0.91,-0.62,1.17,7.05526534938        -       A</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

26

</td>

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

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

<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    21448   TACTTMCCGCA     1.095,0.78,-2.38,1.47,-1.715,-0.828333333333,7.05526534938      -       m6A</span>

</pre>

</td>

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<td class="old_line diff-line-num 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">

27

</td>

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

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

<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    22359   AACTCMAGGTA     -3.59,1.85666666667,-0.96,0.0671428571429,0.573333333333,1.21,7.05526534938     -       A</span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    22558   GAAGAMTCAAC     1.005,3.05,3.07,0.4625,0.32,-0.603333333333,7.05526534938       -       A</span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    23402   GGATTMTTTCA     -0.19,-1.68,-2.3,0.56,-1.41,1.48,7.05526534938  -       A</span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    24474   CTGGAMAAAGC     -1.13,-1.67,-1.1,-0.5775,0.42,1.0225,7.05526534938      -       A</span>

</pre>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    24629   GGGCCMTTACC     0.005,-0.295,-0.54,3.96,1.47,0.065,7.05526534938        -       A</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    24715   GGTGGMTGAAT     3.255,3.925,0.04,-0.156,-1.01,1.35333333333,7.05526534938       -       A</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    24770   GGTTAMCGCGT     -0.08,-1.36666666667,0.84,-0.545,-3.22,-1.53,7.05526534938      -       A</span>

</pre>

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<td class="old_line diff-line-num old" 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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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    25340   TGTGGMGAAAC     -1.74,-2.56,-2.0775,1.84,-0.1,-0.3,7.05526534938        -       A</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template    25919   AGAACMCTTTC     1.92,2.75,1.59,1.64333333333,1.59,1.27,7.05526534938    -       A</span></pre>

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

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

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template       13791   GTAAGMTCCCT     -0.4066666666666667,1.6099999999999999,-1.6866666666666665,6.67,-4.55,1.775,7.055265349382997   -       m6A     0.71</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template       14329   TTGAGMTCCGC     -3.48,1.365,1.06,3.94,1.6,0.98,7.055265349382997        -       A       0.45</span>

</pre>

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

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template       14827   AACAGMTCTCC     -2.38,-2.11,-1.45,-1.4900000000000002,-1.98,0.53,7.055265349382997      -       A       0.1</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template       15249   GCTTGMTCTCT     0.65,2.7,-3.18,1.41,0.76,3.43,7.055265349382997 -       m6A     0.67</span>

</pre>

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

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template       19419   CACAGMTCTAC     1.41,-0.9933333333333332,-2.08,-3.42,-1.5650000000000002,-2.332,7.055265349382997       -       A       0.12</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template       21759   TGGCGMTCCCT     -1.502,-2.01,-2.26,0.5433333333333333,-7.57,-3.11,7.055265349382997     -       A       0.3</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template       22161   CAGCGMTCCGG     2.13,0.7219999999999999,-0.44,-0.08499999999999996,3.9250000000000003,2.86,7.055265349382997    -       m6A     0.71</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template       23875   GTCCGMTCCGA     6.19,-2.07,0.695,2.71,3.575,3.1566666666666667,7.055265349382997        -       m6A     0.56</span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">ecoli 26dd376e-9d82-41fc-921e-71e559c8e8d1_Basecall_2D_template       24559   GCTCAMCGGCT     -0.53,1.9366666666666665,-1.86,0.58,4.6450000000000005,1.17,7.055265349382997   -       m6A     0.85</span></pre>

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<li id="aaafae5b8787053952968171b82158c91258ae8b">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#aaafae5b8787053952968171b82158c91258ae8b"><strong>testdata/masonread1.methylation.summary.bed</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">ecoli 13791   13792   GTAAGMTCCCT     1.0     -       1</span>

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

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">ecoli 15249   15250   GCTTGMTCTCT     1.0     -       1</span>

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<td class="new_line diff-line-num new" 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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">ecoli 22161   22162   CAGCGMTCCGG     1.0     -       1</span>

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

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">ecoli 23875   23876   GTCCGMTCCGA     1.0     -       1</span>

</pre>

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">ecoli 24559   24560   GCTCAMCGGCT     1.0     -       1</span></pre>

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</li>

<li id="e93b7058622f562300a8c44c185746cf72665c8c">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#e93b7058622f562300a8c44c185746cf72665c8c"><strong>testdata/r95_test_read.eventalign.diffs.6</strong>

deleted

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

1

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

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">ecoli f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3647365 TCAGGMCCCGT     0.916666666667,-2.664,-2.25,-0.42,0.135,-1.362,18.3588624525    -       A       0.34</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

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

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">ecoli f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3650835 AATTGMCCGTG     2.48666666667,-0.33,-3.24,-0.69,0.61,-0.955,18.3588624525       -       A       0.43</span>

</pre>

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<td class="old_line diff-line-num 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">

3

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

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">ecoli f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3647734 AAGCGMCCGTC     -0.015,-0.42,-0.96,2.38,0.625,-1.29,18.3588624525       -       m6A     0.65</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">ecoli f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3651075 GCCGGMCCATC     1.81,0.54,0.52,0.902,-0.51,1.91,18.3588624525   -       A       0.09</span>

</pre>

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

5

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">ecoli f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3647914 TGGTGMCCGCG     1.69666666667,1.305,1.24,1.3,0.545,0.025,18.3588624525  -       A       0.24</span>

</pre>

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

6

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">ecoli f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3647968 CGCTGMCCATG     0.6775,-1.24,-3.245,9.47390314347e-15,0.035,-1.57,18.3588624525 -       A       0.47</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

7

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">ecoli f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3651343 TCATGMCCGCC     0.0125,0.19,-1.58333333333,-1.01,-0.35,-2.33,18.3588624525      -       A       0.21</span>

</pre>

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<td class="old_line diff-line-num 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">

8

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

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">ecoli f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3648099 TTTCGMCCTGT     -1.795,-0.255,0.56,1.19666666667,1.69333333333,4.44,18.3588624525       -       A       0.13</span>

</pre>

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

9

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

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">ecoli f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3651484 CTCTGMCCGTT     1.285,-0.0842857142857,2.365,4.36,3.12,2.715,18.3588624525      -       m6A     0.82</span>

</pre>

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

10

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

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3648591 GGTCGMCCAGG     0.235,-0.54,0.225,0.53,-0.753333333333,0.885,18.3588624525      -       A       0.05</span>

</pre>

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<td class="old_line diff-line-num 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">

11

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3651823 CTGCGMCCGGT     -0.336,-0.09,-2.95,-3.43,-0.68,-1.455,18.3588624525     -       A       0.19</span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

12

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

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3651901 AACTGMCCGCC     0.8325,-2.36,-0.705,-1.10111111111,-0.645,-0.703333333333,18.3588624525 -       A       0.1</span>

</pre>

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13

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

</td>

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3651937 CGCTGMCCTTA     -0.505,0.67,-3.07,-0.38,-1.215,-2.92,18.3588624525      -       m6A     0.5</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

14

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3651954 TACTGMCCGGC     -0.195,-0.66,-2.6875,-1.09,-0.976,-3.37444444444,18.3588624525  -       A       0.32</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

15

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3651972 TGCCGMCCTGA     -0.77,-1.61,-2.04,-1.2,0.55,-0.0233333333333,18.3588624525      -       A       0.07</span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

16

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3649911 TAGCGMCCCGC     1.57,-0.94,0.1675,-0.406666666667,0.37,0.68,18.3588624525       -       A       0.08</span>

</pre>

</td>

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

<td class="old_line diff-line-num 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">

17

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3650080 TTATGMCCGAA     3.865,-2.09,-1.09333333333,0.55,-1.2625,-3.34,18.3588624525     -       A       0.5</span>

</pre>

</td>

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

<td class="old_line diff-line-num 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">

18

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3653093 CCAAGMCCGCA     -2.0525,-0.275,-1.91,-0.605,0.62,0.37,18.3588624525     -       A       0.05</span>

</pre>

</td>

</tr>

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

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

</td>

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

<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3653162 AATTGMCCAAC     -1.015,1.06,0.25,-1.05,0.56,0.09,18.3588624525  -       A       0.05</span>

</pre>

</td>

</tr>

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

<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">ecoli        f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template       3653422 CGATGMCCGTG     -1.21,0.04,0.853333333333,2.175,0.44,1.44,18.3588624525 -       A       0.11</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="9f45385b57133f2c2e51ccffe9fa21b8e5fad60c">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#9f45385b57133f2c2e51ccffe9fa21b8e5fad60c"><strong>testdata/r95_test_read.eventalign.tsv</strong>

deleted

</a>

The diff for this file was not included because it is too large.

<br>

</li>

<li id="e5afddf95aabcef3faf8ffe3bd90363102bb9eba">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#e5afddf95aabcef3faf8ffe3bd90363102bb9eba"><strong>testdata/r95_test_read.fast5</strong>

deleted

</a>

<hr>

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<br>

</li>

<li id="2a7716b7749b8b9decac8c9384b3c3f5bd56c724">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#2a7716b7749b8b9decac8c9384b3c3f5bd56c724"><strong>testdata/r95_test_read.fastq</strong>

deleted

</a>

<hr>

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

1

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template r95_test_read testdata/r95_test_read.fast5</span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

2

</td>

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

</td>

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

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

</pre>

</td>

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

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext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<li id="66cb67fd74928240bc37483d0719791d99a853c5">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#66cb67fd74928240bc37483d0719791d99a853c5"><strong>testdata/r95_test_read.fastq.fast5.fofn</strong>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template     testdata/r95_test_read.fast5</span></pre>

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<li id="06d66d35a7ff41745fb371e2045cb01d6b459c75">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#06d66d35a7ff41745fb371e2045cb01d6b459c75"><strong>testdata/r95_test_read.sam</strong>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@HD   VN:1.0  SO:unknown      </span>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">@SQ   SN:ecoli        LN:4734145</span>

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3

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">@PG   ID:graphmap     PN:graphmap     CL:graphmap -r testdata/pb_ecoli_polished_assembly.fasta -d testdata/r95_test_read.fastq -o testdata/r95_test_read.sam  VN:v0.3.0 compiled on Jun 16 2016 at 10:59:07</span>

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</td>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">f88c6bba-5f92-4766-b8cf-21b1af4cc0b1_Basecall_1D_template:1D_000:template     16      ecoli   3646849 40      20M1I56M1I13M1D2M1I42M1D1M2D46M1D20M1I11M3D3M2D45M1I17M2I15M1D9M1I1M1D5M1D32M3I36M2I1M1D12M1I14M1D7M1D17M1D1M1I37M1I4M3I23M1I28M1I72M1I1M1I3M1I33M1D1M1D2M1D5M1I56M1D13M1D33M2I14M1D2M1D3M1D6M1I1M1I38M1I2M2D5M2D10M1D3M1D2M5D7M1D1M1I2M1D19M1D2M1I14M1I12M2I34M1D17M1D12M1I2M1I1M2I27M1I11M3D1M1D1M2D38M1I8M1I3M2D4M1D15M1D60M1I19M1I34M3D10M1D1M1D1M1D44M1D1M1D5M1D10M1D42M1D14M1D1M1D22M1I7M1I2M1I28M1I3M1D3M1D23M1I17M1D18M1D56M1I7M2D13M1I9M3I36M1I1M1D11M2I6M1D23M1I4M1I17M1I11M1I4M1I2M1D14M1D23M2I5M2D12M1D8M3D8M1D6M2D70M2I35M1D25M1D1M1I9M1D13M1D36M1I14M1I29M1D8M1D1M2D14M1D4M1I9M3I11M2D2M1D2M1D7M1D39M1I2M1I26M1I19M1D4M2I1M2I4M1D10M1D19M2D1M2D17M2D24M1D30M4I1M1I6M1D14M1D1M1D3M2I9M1D31M3D2M1I1M1D37M1D48M1D3M3D6M1I2M1I21M1D22M1I10M1D1M1D12M2D35M1I1M1D46M1I2M2D6M1D1M1I3M1D3M1D34M5I16M1I9M1I1M1I23M1D23M2I1M1I12M1D2M1D4M1I4M1D13M1I2M1D14M1D26M1D62M1D34M1I30M4I18M2D6M1D20M3I9M1D1M1I2M1I28M1D2M1I1M1I41M2D42M4D15M1D27M1D17M1I1M1I2M1D24M1D6M1I2M3D33M1D1M1D19M6D2M1D9M2I2M1I2M1D2M1D2M1D3M1D6M1D17M1I27M1I14M1D13M3D16M1I3M2D2M1D25M1D25M1D15M1D1M1D1M1I5M1D3M2D6M2D6M1I1M1I2M1D3M1I15M1D10M2D31M1I25M2D36M1I22M1D13M2I1M1I52M1I20M1D26M1I11M3D16M1D17M1D2M1D2M1I1M1D30M1D13M1I47M1D12M3D3M1I15M1D2M1I2M1D16M1I22M3I72M1D14M3D3M1D5M1D11M2I1M2I2M1I2M1D20M1D8M1D26M1D20M1D5M2D7M4D1M1D3M1D1M1D2M1I1M1I3M1I1M1D2M2D19M1D13M1I7M2I12M1I14M2I6M1D33M1D12M1D36M1I6M1I1M1D4M1D13M2D2M1D39M3I2M1D24M1D8M1I5M1I1M1I7M1I13M2I30M2I11M1D5M2D6M2I24M1I50M1I1M1D3M2D9M1D19M2D11M1D17M1D7M1D34M2I1M2I18M1I9M1I1M1I2M1I55M2I52M1D20M1D3M1I1M1D3M1I76M1D8M8D15M1D1M1D2M1I7M1D9M1D20M1D22M1D7M2I38M2D21M1I7M2D6M1D43M1D35M2D20M1I3M1D8M1D23M3I6M1D1M3D12M1D30M2I12M1D34M1I2M1D3M5D6M1D11M1D3M1I8M2I6M4I17M2D2M1D1M2D1M1D31M1D55M1D4M1I64M1D20M1I10M4I10M2I3M1I12M1I1M1I26M1D12M1D9M3D33M1D32M1D3M2D16M1I3M6D9M1D6M1D2M3D27M2D6M1D39M1I15M1I1M1D33M1I51M1I4M1D22M2D2M1I2M1I2M1I14M1D14M1D1M2D2M1D15M1D28M1D8M2I36M1D29M2D6M2D1M1D7M2D13M2D23M1D1M1D26M1I7M1D5M1D2M1D25M1D2M1I5M1I1M1D11M1I20M1D47M1I2M1I14M1I3M2D15M1I8M1I16M1D4M1I16M2I16M1I35M1D5M1I10M1D8M1D21M1D2M1I8M1D25M1D19M1D1M1D5M1I1M1D15M2I10M1D4M1D15M1I3M1I9M2I1M1D2M1I1M1I4M1I3M4D9M1D31M1I1M1I38M1I4M1I17M2I1M1I2M1I6M1D6M1I3M1I16M1D18M4I1M1I3M2I10M1I10M1D13M1D16M1I8M1I1M1I7M1D11M1I2M1D2M1I2M1D4M1D22M1I30M1I1M1I1M1D10M2D21M1I6M2I5M1D6M1I7M1D1M1I20M1I4M1I8M1I1M  *       0       0       ATGACGCAGGACGATACCGCGGATCGCTGACGCCAAGCGCCTGTGCCGCACGAATGTAGTCGAAATTACGAGTACGTAAAAAACTCCGCCCAATCCACGCCGACCAGACTCATCCAGCCAAACAAGACAGTAATTGCCAGCCACCAGAAGTTAGGCTGTACGACGCTGGAAAGCAAAATAATCAAAACAGCGTCGGCATCCCCGGACCATACTTCACAGTTAACCCCAGAGATCGACTTTACCGCCGTAATAGCCTTGTAGCGCCCCCCGCCAGCACGCCCATATCACGCTGGAACAGGAGTCAGCACTTGTACAACAGAACCGAGATCCGCGTGCCATAGAGAATAACGTGTGCCAGCACATCGCCGCCGTTGGCATCCGTTCCTGCGCCAGTTTTGCCGGGGAGGGTGGAGAAGGAAGGGTCATTGGTAGCAAAGTTACTACTGGTAGCACCAAAGCGGTTCGGTGCCCACAGTACTCCAGCCACCGTTATTTTCCAGCCGTTGTTTCCAGCCACGGGTCCCGATAATCAGCCTGACCTTGCCAGCGGGCCGCCAAAATCGCTTTCGCTGTAGTTTTTCAATAACGGGAAATACCAACTGCCGTCATAATCTGAATTCAGCAACGGTTTATCGTTGGCGATAAGTTCAGAACAACTCAAAACCAAACAAGACGAGGAAAATCCATAACGACCAGTAGCCGCGATGGTTATGACGAAACGCGCCCAACGGCCTGATTGACGGGGCTGAGTCGTGACATTAACGCGTCCCTCAAAATCATCACGATCAACCACAGCGTATAGCCGATATCACCGACAATATTCAGCAGCATTGAACCAGTGAAAATATTGAGTGCAGTGCGTGACACCGCGCGAGACGGTCGCTCTGCAGTCCAGTAAGCTCCAGACCATTGAGCGCGAAAACATCACCTCAATCAGCAGCGAGCCGGTAAAAACATGCTGATAAAGTCGCCGGAAAACCCGGCAGCAATCACCAGCAGCATGGCGTTGCGGAAACACATGTTTGGTATATTTTTCACTTACCCCTTTCGCACGCGCGGTCACCAATGTATTGTCATGCACTCATCAAGGAATGAGTTTTTGTCAGCATGGTCAGCGCCGCAAAGCCACCAATCACTGTCGCCAGCACCGGCAGCGCGGATATGCCGCTGATAATCTGGTGATTTTCTGATGTCACGGCAGCGAATCAAAGGCGCAAACCAGCTGTAGAGGGAACAGGTCGAAATAGCTGCCGCCCGCGAAGAAGACACCGTAGATGGCAAACAAAAGGCCGGAATGGCGTAGCCGATGATGATAAATGCGCTACCCAGACGTCAAAGCGTTCTATTATAAACAGCTTTATGAAATGCCTAAATCTGAATCGACACCAGATAGATAATCAGCAAAGTTCCAATCCGAGGGTGATGGAAACCGCGGTGACTGTCTTTAATCGCGTCAGCACCGAGGCGCGCGAAACAGGCTATCGCCAAAATCAAAGCGGATGTAGTCCCAGAGCATTTTGGTTTAAACGTTCGGATCGGCTTATCAAAAACCGTAAAGGATATGAGTGATCTCAGCGATCACTTCTGGATCTAACTGGCGTCCGCCAGCCGGTAATACTGTCGCTGATATTGCCGACACCCCGTTTTGCGCATGGCTGGCATCGAACACCTTCTACCGTTCGCGCCGGGCAATACCCGGCATTACCAAACTCAATGGCGTGGCGAGACTGGTCGACCGACCGCCAGTAATTTGGCGATGAAAGTTGATGGCGATAATCGCCCATAATGTTGGGATCACCAGCAACAGACGGCGAATCAGGTAAGCGCCCATATCTACTCTCCCTGTTTGCTGGCGGACGGCAGTTTGCCGTTTTATTGACGTCATACCACCGTGTATCGATACGAGGCTATAGATGGGTGCACGGCCGGCTGGGAGAATTTATCCCACCTGTGCGAGCCTATCTTCTCGCCATGTACCACATTGGCAGCATGTAATATTCCACGTTACGCGATCCAGTGTCGCTCCCAACGGCAAAAGTAATTTTTCTATTCCTGCGCGCAATAATTTGGTTGATCAGCGAGTCGATAACCGGGCTTCAGTAACGCCGGGGGCATTATAAGTGGAATCTGATATATTCTGATGACCAGAAATCTAACTGTAACCGGAACTGGCCACGGCATCGCCCGCCACGCGGCATCATGTCATACGCGACTGCGCATGCGGTTAGTGACGGCGAGTTATCCACCTTGCGAATGTCCATAAGCGCTGGATACCAGCCGTTGCAGGTTGCAAAGGAACGGCATACCCACTGACTATTGCTGCTTGCGGGAAGTACACCAAAGCTGAGTGGCTGACCCGTTGTGGCATTAACGCATGCTGACCCTTCAGCACCCAGCCCGCTTCGTTGAGAAGTTTGTCGGCTGTAGGTTGTTCGCCGATCGTAGCCATCGCCTTTGATACCGGCGGCTGGTGGATTTGGTGTGAAGACTTGACGGTAGATCTTTTCATTGGTGCCAGAAGCACCAGCTCCGCGGCGCTGGGGTAATTTCTGGCCGCGTATTCGGTATTCTGAAAATAACTGTTCAGTGACTCCGTGCATGTAAACAACGCCTTGTTCATCCATTCAAAGTCAAAGCAGGCGCGAGAGTGATAGCTTCCCCGGACCCGGCGCGATCGCTGAATACCGGACGTTGATATTAAACGCCAGCCAACGCGTATCATCCCGGGCTGATCTTGTCTTTGTCATCTTTGATGACAGCTTTTTTATCGAAATTTTACCGGTATAACGCGTGGCCCAGTTTTGGCGTCGTTTTCCATACGCAAATCAAAGGCACCTGCTTTAAACGCTTCAAAGGCGACATATCATCGAGGTAATAATCGTAGCGAATGGTGTCGGAAATTCCAGCGTCCACGGTTTACCGGTAAGTTTGTTTGTTGCCCAGCAATCTCACACGGAACAGACAATATTCGGCCATTCCATCTTCCGTGATCGTAACGCGGCATGGACCACTGGCAAGCGAGGCGCGTGGCGAGCGGGTCGCTAAGTTTGTGATCCTTCCAGTACTTCTGGAAATACCGGCAGCGAAAACAGACTCAGCATATCTTCACGGGTTTAGCTAACCAATGCGCACGGTTAACGGTGCAATGGTTTGACGGTGGTGCCTTGTGGTGACCAGACGAAATTGCGGCACGCCTCGGTCGGTGTTTTGAAAAGTAAACTCTACATCGCGGGCAGTACGGCGAACCATCATGAAAACGGGATTAATAGTGCGGACTCACCAGAATAACGTCAGCATAGCGTGCGCCTTTCAGCAATCAGCGGGTAATAACCGCCCCGGTTCGTCATCGAAGTCGCAAATATGTCGTACAGTTGCTCAGGTGTAGCCTGGGTTGCCGCGCAGCGCATATGGTTGAAATTATCGAAGGTGCCGATATTGATAACGTTATTCACCACCTTTAGTGGCGGTTCAGCGATACCGGTACCGGTTGAAATTAACGCGTACCGGTTCGCCCAGCACGGCAAAGGCATAGCTTTCCCTTGATAGCCTGCGCCTGCACACCAGCAGAACAGAGCGATAAACAGCAGCAGTATGCGTACCAATCATCTGCAACGGATTTCCTTTACTCATCATTAAATGCCGCAATCCGGCATGTTTTCACCATGAATAATAAGGGACGTAAGCACACCTGCACCACTGCGGCGTATACAGTTCTTTAGCCAGCGAACAAAATCGTCTCAGCGGTAACGTGTTAATCCAGTAGCCTGCATGAAATTAACGTCAGTCTGTTAGCCATCGCGCCTGTTCCGGCGTTTCGACCCTTCAGCAACCAGTCAGCATATTGAGGCGTTTCGCCAGCGTCAGCACCGCGTCAAGTACGGGGAAGTGATCACCTGTACCGATGGCGCTGTACAACCACGGTCAATTTTCAGGATAATCGAGCGTAAAACGCTCAATAAGATAGATAAGCGCGCTGTGCCCGGTGCCGAAGTCATCAATAGCAATTTCTACGCTGACCGAGTGCAGCCAGCGAAGAGTTGTATTTCTGCTCTTCAACATATCAGGCTCGCCTGGTAATTTCCAGCACAATCTGAACTGGTAAAGGGCAGGGAAGTGAGCAGTTTCTGATATCTGTTTTAAAGCTTTACAGTAGATGGTCCAAGTACATTACTCAATGACGCCCAACAGCAGCACTTTTCTAATTCTGATGGCATCAAGTGGGCAATTAACCTCAAACAGGTGCTGAGAGTCATGGCACAATCATCTTTTGCGATTCGGCAAAGTTGTGAAGGCATCCGGGGAATTTCTCCCGTGACAGGATGCCGCCAGCGTAGGCAGTATCTCCAGCCCGTTACTCGCAGTTTTGTATCCACCACCGGCTGATACGCCACGTAAAATTGAAATTGCGCTTGATGGCGGTCATGATTTCCTGCCGGGTGCATACTGACGCACGCCTCATCAGGTAATAAAGCAGAGCAGGCCAACGACAGTTCCACTCATGTGCCGCCCAGTAAAATGTAACATTAATATCGTTCCATGTCCAGTCATCTTGTATAAAGCCGAACGGTCAGAGGAATGCCCGCAATTTTAGTTTCACGGATCAGCGTCGGTTAATCGTTAACGTTCATCAAACGAAGAAAAGGTGATAGCGCAGTATTGCCACAATGAGGCGACGCCATCGTAATCTTCCCGCCGTGAACTATGTAAAAAAGAGTGAAGGCGTCAGGGTTGAGATCTGGAGGAGCGGCAAAGACGCCGCTATTTTTCAGCAAAGGGCTGCGATACCAGATGACGATACTGCGGGTTTGTTCGGCACCATCGGCGTGCCGGGTAAGATCGCCATATCGACGTTTTATTAATGTCGAGCGCCGAACTAATCTTATTGAGTGGAATGTCCATCTCACCGGTCGCAGATGAACAGAATGTTTTTTTATCTTTCACCAGCACAAACGTTCGACATTCAGCTGCGCGGGCGGTCGTCTGAAGTTACTTGCTGGCGGCATCTAAGGTCAGCGGCTGAGCCGGTCAGTAGTGGATTTCGGTCGGCAAAAAATAGGTATCGAGATACTTTTGTACGCCGGTAATCAGTGTCGTATTTGACTTCGTGCTTTATGCCGCCACTAAAACTGAAGGCAACTCACCAGTATCGTAATCATTACGCCTGCACAATGCAGGTAAGCAGGAGCTTACGTCCAAAATTGAGCGCGTATGAACATGATTCCCGTAATTTCCGAAATTAATACAACATTTAAAAGATAATAACATCGGACTATAGCCCGATCAAGACGCGGAAACATCATTTTCTCTGGGATGAATGAACAAAAAAAGCACCGCCTAAGCAGTGCTTTCAGTTAACCTGTCAGCCAAGGATTGCATCCAACAGGTTTATTGGGGCTGCAAGTGGCTGAGAACCCGGCGTTTGGCACGCTTCTTCCAGTACGGTTCATTCATGCTGAAATAATAACACCACTGCTGGTGGAAGCATTGACAAACTGATTGTTGCCGATATAACAGCCGACATGGCGTCCCGTTGAACTGGCACGGAACAGAACTAAATCACCCGTACGCAAATTACCGCGGAAACAGATTTACCCATTTCCCTGCTGTTCGTAAGTAAGTCGAACGCGCGGGAAGTTCTAAGCCACAAATTGCTCACGGAATGTACGCTGTCGAAACCAGAACACCGATACCTTTAGTGCTGCCGCCCAGACGATAACGTACGCCTTCCAGTCAGCATACTGATCCATAATTCGCGATTTGCCGACATTACGAACCAAAGAATTCATCCGAGAAGTTGTGATGATGTTTCACTACCCACTGCACGTCTCAGATGCATATTCTTTGCGGTGTTATTTGTACTACATGCAGAAAAGCAGAACTGCTATCAAAATCGTGGGAATCCCGCGCAAGATATATCTCAAAAATCGGTTGAGATTTGACCATGTTGTTTGTTTTCCTTTGAAGTCCTTAACCGACAACATCGTTATAAAAAAACGCCGCTTATCATCGAGACCACTTACCCGGTATGTTGAAACACCTAAGGCCAAATCTGTGACCAACGCACAAAATTATATGCTGTGAGATAATCTCCACCGCCGAGGCAAAACGAGTTCGAGATTACCCGATTGCGCGGTCTTGGCGAGCGGTTTTACATGATTTTATGCTAAGTGACAGAAAGTTACTGCTGGGTTGGTCAATTAAAGTACACGAGTGAAACGCATGCAATCCATTCATTTTAATTTAGAACATTTTGCGTTCGATAGATGAAAGTACGTAGTGCACTATCAGGATTATCCCTTACTATGTACGTAACCCGATGATGTTAATTACTGTGAGTTATTTGTTTTGGAAATGTTTGTTTTCTTCCCCGGTAGTGATTTATTCAAAAGGTGATTAATCTGATCACTTCAATGGCGTCAGCAACACCTGTGGCAAACCGATCAATACTTCACGGTCATCGAACCTGACAATGATGTCAGTAAACCAGTGTGCGCCAATCATACTCAGGGGAAATGCAAAACCACAAAATAATAAGGGCGATAAGGCTCGTAACTTTACGAAATAACGCCACATGAATGCCGGAAAACAAGGTGCATCATGCTGAACAGCGGGAAAGCTATCTCGTGTGAGGTATCTTCGGGGAACAGAGAGCAGTTTCTGCTGACGCGAAGTACATTATCAGGTGTCACCGTTGGCTGGCCTGTTTTACAGGAATTACCGCCTGAATTCCAGCTGGTTTAATACCACCGCAGTTAATAGCATGACTCAGACCCAATAATCACGATACGCTTCCGTTCCGCCGTGGCGCTTTCTTTTTCAGCCAGAAACCAGTACCAACATACCCATATCGCTGCCAAAGCAGTGAACAAACTGTCGAAGCGCGATTGTTGGCCACGCAACCAGCCACAAAAAAGGCTCTTTACTTTGACCAGTTTCTGGACAGTAAAATAAAAATATCCTAATCAATCGGCAAACGTGAATCCATGATTAACGGGGATATACTCGAAAAAGAAACAGCGAGGCCGACAATATTCGTCAAATACTACATTTGGTAAAATTTTTTAACGATATTTTCTCTAATTATCTTTACCGGAAAAACGAGA ,*/11:989@B,1+,,+15.12+*,/)08340D/</64?E3,00/2-:6=/BG@<CDE?>55=@2071159<=BBD:5FD59;+):5?<20).)?>?;=@7@DC<9<;91>BCF==:D:DG=170+(,-*(*0)&*))&(&(++-)/-+(*()0/-0</53@7982./53849.?DE96<;8.>BE=;E@@EDE@F<F@9D@<)?69??93,()+4'+*((/,*.-.-233105<A1;@500-49.6.>B=>21-/,0//99>,?DC0+;9<?ACEB=?91*'+,12=A,++6.6-*.6--*-*1+,'**+**(.4-17DB@2=>>AAE<;<?@>D:;7?DD:<2+3/-3)3323/4:3?/)'./&032(<7901'11@:;9;18++&**=;;6=F;8505E@28<?=:DCADE5;@>=31-&(+1C5=<?2.33.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<li id="f4697d3b351cb1b8662ba7fe39d77865b0c5da1a">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#f4697d3b351cb1b8662ba7fe39d77865b0c5da1a"><strong>testdata/r95_test_read.sorted.bam</strong>

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<li id="a87b5a1e5dc83636a2957fd0c3abeee07d17173a">

<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#a87b5a1e5dc83636a2957fd0c3abeee07d17173a"><strong>testdata/r95_test_read.sorted.bam.bai</strong>

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<a href="https://salsa.debian.org/med-team/mcaller/-/compare/ecb0a82fb9d37058ece6e50d3e32aff5e68f4986...20ee86e6cad7216386777daa4da1f0fc87213e96#85d3313fac8bf1ae2cd49e275fe72905c0f5ed05"><strong>train_model.py</strong></a>

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">cPickle</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#import _pickle as cPickle</span></span>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pickle</span> </span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">numpy</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">np</span></span>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">plotlib</span> <span class="kn" style="font-weight: 600;">import</span> <span class="o" style="font-weight: 600;">*</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"><span class="idiff left right">#</span>from plotlib import *</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.model_selection</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">RandomizedSearchCV</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.model_selection</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">GridSearchCV</span></span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">sklearn.ensemble</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">RandomForestClassifier</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -86,9 +85,9 @@ def train_classifier(signals,groups,modelfile,classifier='NN',plot=False): #TODO</td>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python">            <span class="n" style="color: #333;">sigs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sigs</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">signals</span><span class="p">[</span><span class="n" style="color: #333;">twobase_model</span><span class="p">][</span><span class="n" style="color: #333;">label</span><span class="p">][:</span><span class="n" style="color: #333;">num_examples</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">            <span class="n" style="color: #333;">grps</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">grps</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">groups</span><span class="p">[</span><span class="n" style="color: #333;">twobase_model</span><span class="p">][</span><span class="n" style="color: #333;">label</span><span class="p">][:</span><span class="n" style="color: #333;">num_examples</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">labs</span><span class="p">[:</span><span class="mi" style="color: #099;">10</span><span class="p">]</span></span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">sigs</span><span class="p">[:</span><span class="mi" style="color: #099;">10</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left right"> </span><span class="n" style="color: #333;">grps</span><span class="p">[:</span><span class="mi" style="color: #099;">10</span><span class="p">]</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">labs</span><span class="p">[:</span><span class="mi" style="color: #099;">10</span><span class="p">]<span class="idiff right">)</span></span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC89" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">sigs</span><span class="p">[:</span><span class="mi" style="color: #099;">10</span><span class="p">]<span class="idiff right">)</span></span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC90" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left">(</span></span><span class="n" style="color: #333;">grps</span><span class="p">[:</span><span class="mi" style="color: #099;">10</span><span class="p">]<span class="idiff right">)</span></span></span>

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python">        <span class="n" style="color: #333;">scores</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cross_val_score</span><span class="p">(</span><span class="n" style="color: #333;">model</span><span class="p">,</span><span class="n" style="color: #333;">sigs</span><span class="p">,</span><span class="n" style="color: #333;">labs</span><span class="p">,</span><span class="n" style="color: #333;">cv</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">gfk</span><span class="p">,</span><span class="n" style="color: #333;">groups</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">grps</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" 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">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"%s %s model scores: %s"</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">classifier</span><span class="p">,</span><span class="n" style="color: #333;">twobase_model</span><span class="p">,</span><span class="s" style="color: #d14;">','</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">s</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">scores</span><span class="p">])))</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -109,7 +108,7 @@ def train_classifier(signals,groups,modelfile,classifier='NN',plot=False): #TODO</td>

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

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">            <span class="n" style="color: #333;">plot_training_probabilities</span><span class="p">(</span><span class="n" style="color: #333;">prob_scores</span><span class="p">,</span><span class="n" style="color: #333;">twobase_model</span><span class="p">)</span>      </span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<td class="new_line diff-line-num" 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="python"></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python">    <span class="n" style="color: #333;">modfi</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">modelfile</span><span class="p">,</span><span class="s" style="color: #d14;">'wb'</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

112

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<td class="new_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(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="LC112" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">cP</span>ickle</span><span class="p">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">models</span><span class="p">,</span><span class="n" style="color: #333;">modfi</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="python">    <span class="n" style="color: #333;"><span class="idiff left right">p</span>ickle</span><span class="p">.</span><span class="n" style="color: #333;">dump</span><span class="p">(</span><span class="n" style="color: #333;">models</span><span class="p">,</span><span class="n" style="color: #333;">modfi</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" 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="new_line diff-line-num" 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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<pre style="margin: 0;"> <span id="LC112" class="line" lang="python">    <span class="n" style="color: #333;">modfi</span><span class="p">.</span><span class="n" style="color: #333;">close</span><span class="p">()</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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<td class="new_line diff-line-num" 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="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">models</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="115" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

115

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<td class="new_line diff-line-num" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

114

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"></span></pre>

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