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GitLab

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<h3>

Andreas Tille pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/a8ef77dcdc095777f530cd797e1abf0bc9572d22">a8ef77dc</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-10-01T15:13:12Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.0+dfsg</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/0ba24d6df37687d760e59d76115507a495444ec9">0ba24d6d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-10-01T15:13:12Z</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/fc46022567edfea7b86beacc66b6ab0088c8168b">fc460225</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-10-01T15:13:12Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.1.0+dfsg'

Update to upstream version '2.1.0+dfsg'

with Debian dir 955646f472dfa57207935caf795a978a466f52c9</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/f5ef3364a8f51dc70bcafc812c0633d7b1d079c3">f5ef3364</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-10-01T15:33:41Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adapt patches - upstream took over 2to3.patch

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28">43e9ade9</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2019-10-01T15:34:39Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version closes Python3 bug

</pre>

</li>

</ul>

<h4>21 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

README.md

</a>

</li>

<li class="file-stats">

<a href="#806a2eb8d45517373c81701d49fefdfd30e648c5">

bin/mapDamage

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#555c85016bd79aa8bbb523506af81b69d9c69534">

<span class="deleted-file">

−

debian/patches/2to3.patch

</span>

</a>

</li>

<li class="file-stats">

<a href="#88645f50aec6faa6b6917074e6c75473dad1acb5">

debian/patches/fix_quantile_na_rm.patch

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#04da551d7b8b96ce0f039c05c3a01a8f3590d1a0">

debian/patches/use_debian_packaged_seqtk.patch

</a>

</li>

<li class="file-stats">

<a href="#2d6120769b574994bf02fb43949cb89bc2e2c36c">

mapdamage/Rscripts/mapDamage.R

</a>

</li>

<li class="file-stats">

<a href="#d97202d39b17c50fc83c976a09e5c652fcdb217c">

mapdamage/Rscripts/stats/function.R

</a>

</li>

<li class="file-stats">

<a href="#107569f6853a50f9e86ad7b15639ea4b3fd398b4">

mapdamage/Rscripts/stats/main.R

</a>

</li>

<li class="file-stats">

<a href="#a42a42a3de2ad00a1423a75f0791ae4dd1737b53">

mapdamage/__init__.py

</a>

</li>

<li class="file-stats">

<a href="#4481def45a752330bb6f29dd87ff5a798f79aeb2">

mapdamage/align.py

</a>

</li>

<li class="file-stats">

<a href="#401cd204f5537ece913ab718c203d3b6c6248caa">

mapdamage/composition.py

</a>

</li>

<li class="file-stats">

<a href="#88a1d21eb50ece62b8a9d89ea1dcbc165188579f">

mapdamage/parseoptions.py

</a>

</li>

<li class="file-stats">

<a href="#a30b6a3b0ae4d9941d25e49d20f6a1a496380bc4">

mapdamage/rescale.py

</a>

</li>

<li class="file-stats">

<a href="#75b02a5c976ccbaf5ae0eb096d80048de9e6c6d5">

mapdamage/rescale_test.py

</a>

</li>

<li class="file-stats">

<a href="#017dc3d29c7a52f7f3babb6888efcd4925648636">

mapdamage/rscript.py

</a>

</li>

<li class="file-stats">

<a href="#f1abf675c9546a833e1e6a8ab63806c189f1d0e5">

mapdamage/seq.py

</a>

</li>

<li class="file-stats">

<a href="#e355b413f51f144a95b8d6b33f74ce254bdbbdd2">

mapdamage/tables.py

</a>

</li>

<li class="file-stats">

<a href="#65134f9708e381a1019a789ae57129129e967d80">

mapdamage/version.py

</a>

</li>

<li class="file-stats">

<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">

setup.py

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>

<hr>

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

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

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

1

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

1

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Important</span></span>

</pre>

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

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

</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="markdown">Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of <span class="idiff left right">mapDamage</span> to use half of the data for estimation of the damage parameters, sorry for the inconvenience.</span>

</pre>

</td>

</tr>

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

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

</td>

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

2

</td>

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="markdown">Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of <span class="sb" style="color: #d14;"><span class="idiff left right">`mapDamage`</span></span> to use half of the data for estimation of the damage parameters, sorry for the inconvenience.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

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

</pre>

</td>

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

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

4

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

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Introduction</span></span>

</pre>

</td>

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

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

5

</td>

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

5

</td>

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown">Complete documentation, instructions, examples, screenshots and FAQ are available at <span class="p">[</span><span class="nv" style="color: #008080;">this address</span><span class="p">](</span><span class="sx" style="color: #d14;">http://ginolhac.github.io/mapDamage/</span><span class="p">)</span>.</span>

</pre>

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

6

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

6

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

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

</pre>

</td>

</tr>

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

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

7

</td>

<td class="diff-line-num new_line 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">

</td>

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

<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">mapDamage2</span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/publications/mapdamage2.0/</span><span class="p">)</span> is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns<span class="idiff left right"> </span></span>

</pre>

</td>

</tr>

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

8

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown">among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.<span class="idiff left right"> </span></span>

</pre>

</td>

</tr>

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

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

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">mapDamage2</span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/publications/mapdamage2.0/</span><span class="p">)</span> is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns</span>

</pre>

</td>

</tr>

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

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

</td>

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

8

</td>

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown">among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.</span>

</pre>

</td>

</tr>

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

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

9

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

9

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

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

</pre>

</td>

</tr>

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

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

10

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

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="idiff left right">Mapdamage</span> is developed at the <span class="p">[</span><span class="nv" style="color: #008080;">Centre for GeoGenetics</span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/</span><span class="p">)</span> by the <span class="p">[</span><span class="nv" style="color: #008080;">Orlando Group </span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/research/research_groups/palaeomix_group/</span><span class="p">)</span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="sb" style="color: #d14;"><span class="idiff left right">`mapDamage`</span></span> is developed at the <span class="p">[</span><span class="nv" style="color: #008080;">Centre for GeoGenetics</span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/</span><span class="p">)</span> by the <span class="p">[</span><span class="nv" style="color: #008080;">Orlando Group </span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/research/research_groups/palaeomix_group/</span><span class="p">)</span>.</span>

</pre>

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

</pre>

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

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

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

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="markdown">Anna Kostikova from <span class="p">[</span><span class="nv" style="color: #008080;">insideDNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://insidedna.me</span><span class="p">)</span> implemented a web interface for mapDamage.  </span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown">Users can adjust the cloud res<span class="idiff left right">s</span>ources in terms of RAM/CPU to perform their analysis. She wrote a <span class="p">[</span><span class="nv" style="color: #008080;">tutorial</span><span class="p">](</span><span class="sx" style="color: #d14;">https://insidedna.me/tutorials/view/Analysis-ancient-DNA-samples-using-mapDamage</span><span class="p">)</span> explaining how to use this <span class="p">[</span><span class="nv" style="color: #008080;">web interface (sign up required)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://insidedna.me/app#/tools/100648/</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">Users can adjust the cloud resources in terms of RAM/CPU to perform their analysis. She wrote a <span class="p">[</span><span class="nv" style="color: #008080;">tutorial</span><span class="p">](</span><span class="sx" style="color: #d14;">https://insidedna.me/tutorials/view/Analysis-ancient-DNA-samples-using-mapDamage</span><span class="p">)</span> explaining how to use this <span class="p">[</span><span class="nv" style="color: #008080;">web interface (sign up required)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://insidedna.me/app#/tools/100648/</span><span class="p">)</span></span>

</pre>

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

</pre>

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

</pre>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Citation</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,5 +31,4 @@ http://bioinformatics.oxfordjournals.org/content/27/15/2153](http://bioinformati</td>

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

</pre>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Contact</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown">Please report bugs and suggest possible improvements to Aurélien Ginolhac, Mikkel Schubert or Hákon Jónsson by email:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown">aginolhac at snm.ku.dk, MSchubert at snm.ku.dk or jonsson.hakon at gmail.com.</span>

</pre>

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

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<td class="diff-line-num new old_line" 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="LC34" class="line" lang="markdown">ginolhac at gmail.com, mikkelsch at gmail.com or jonsson.hakon at gmail.com.</span></pre>

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<br>

</li>

<li id="806a2eb8d45517373c81701d49fefdfd30e648c5">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#806a2eb8d45517373c81701d49fefdfd30e648c5"><strong>bin/mapDamage</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/<span class="idiff left right">python</span></span></span>

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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/<span class="idiff left right">env python3</span></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;"># -*- coding: utf-8 -*-</span></span>

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<td class="diff-line-num new_line 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">

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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;">__future__</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">print_function</span></span>

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

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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;">logging</span></span>

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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;">random</span></span>

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

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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;">time</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -37,7 +35,7 @@ plot and quantify damage patterns from a SAM/BAM file</td>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;">:Date: November 2012</span></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"><span class="s" style="color: #d14;">:Type: tool</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"><span class="s" style="color: #d14;">:Input: SAM/BAM</span></span>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="s" style="color: #d14;">:Output: tabulated tables, pdf<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"><span class="s" style="color: #d14;">:Output: tabulated tables, pdf</span></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># check if pysam if available</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -45,7 +43,7 @@ MODULE = "pysam"</td>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"><span class="n" style="color: #333;">URL</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"http://code.google.com/p/pysam/"</span></span>

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<pre style="margin: 0;"> <span id="LC44" 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="LC45" class="line" lang="python">    <span class="nb" style="color: #0086b3;">__import__</span><span class="p">(</span><span class="n" style="color: #333;">MODULE</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p"><span class="idiff left right">,</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">as</span></span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>

</pre>

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

49

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python">    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Could not import required module '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s':</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">- </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">MODULE</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">))</span></span>

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python">    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"       If module is not installed, please download from '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">URL</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python">    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"       A local install may be performed using the following command:</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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<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="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -98,7 +96,7 @@ def _downsample_to_fixed_number(bamfile, options):</td>

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<td class="diff-line-num old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">index</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">downsample_to</span><span class="p">:</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">                <span class="k" style="font-weight: 600;">continue</span></span>

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

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python">        <span class="n" style="color: #333;">sample</span><span class="p">[</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span></span>

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

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<td class="diff-line-num new_line old" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC101" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">filter</span></span><span class="p"><span class="idiff">(</span></span><span class="bp" style="color: #999;"><span class="idiff">None</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample</span></span><span class="p"><span class="idiff right">)</span></span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">_f</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">for</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_f</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">sample</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">if</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">_f</span></span><span class="p"><span class="idiff right">]</span></span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="python"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_read_bamfile</span><span class="p">(</span><span class="n" style="color: #333;">bamfile</span><span class="p">,</span> <span class="n" style="color: #333;">options</span><span class="p">):</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -116,12 +114,12 @@ def _read_bamfile(bamfile, options):</td>

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

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

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

</pre>

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

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC115" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_check_mm_option</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC116" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;">    As the user can override the system wide mapdamage modules with<span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="python"><span class="s" style="color: #d14;">    the --mapdamage-modules, it has to happen before option parsing<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC117" class="line" lang="python"><span class="s" style="color: #d14;">    As the user can override the system wide mapdamage modules with</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="python"><span class="s" style="color: #d14;">    the --mapdamage-modules, it has to happen before option parsing</span></span>

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="python"><span class="s" style="color: #d14;">    in mapdamage.parseoptions</span></span>

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

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="python">    <span class="n" style="color: #333;">path_to_mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">None</span></span>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nr</span><span class="p">,</span><span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">xrange</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">argv</span></span><span class="p">)),</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC122" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nr</span><span class="p">,</span><span class="n" style="color: #333;">arg</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">range</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">len</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff right">)</span>)),</span><span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">arg</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">"--mapdamage-modules"</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC124" 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="LC125" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="s" style="color: #d14;">"="</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">arg</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -130,7 +128,7 @@ def _check_mm_option():</td>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="python">                    <span class="n" style="color: #333;">path_to_mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">arg_p</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="LC129" 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="LC130" class="line" lang="python">                    <span class="c1" style="color: #998; font-style: italic;"># the option is of the format --mapdamage-modules AAAA</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python">                    <span class="n" style="color: #333;">path_to_mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">nr</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python">                    <span class="n" style="color: #333;">path_to_mm</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">nr</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="python">                <span class="k" style="font-weight: 600;">break</span></span>

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<td class="diff-line-num old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="python">            <span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">IndexError</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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<td class="diff-line-num old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python">                <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Must specify a path to --mapdamage-modules"</span><span class="p">)</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -201,7 +199,7 @@ def main():</td>

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="python">                <span class="n" style="color: #333;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">composition</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_base_comp</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ref</span><span class="p">,</span><span class="n" style="color: #333;">path_to_basecomp</span><span class="p">)</span></span>

</pre>

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

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<td class="diff-line-num new_line" 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;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rscript</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run_stats</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" 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">

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

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="python"><span class="idiff left right">    </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC202" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># fetch all references and associated lengths in nucleotides</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="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="LC205" class="line" lang="python">        <span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Fastafile</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ref</span><span class="p">)</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -230,7 +228,7 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python">        <span class="n" style="color: #333;">in_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>

</pre>

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

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

</pre>

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

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

</pre>

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<pre style="margin: 0;">-<span id="LC233" class="line" lang="python">    <span class="n" style="color: #333;">reflengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">in_bam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">references</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">in_bam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">lengths</span></span><span class="p">))</span></span>

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<td class="diff-line-num new old_line" data-linenumber="234" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC231" class="line" lang="python">    <span class="n" style="color: #333;">reflengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">in_bam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">references</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">in_bam</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">lengths</span></span><span class="p"><span class="idiff right">)</span>))</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># check if references in SAM/BAM are the same in the fasta reference file</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python">    <span class="n" style="color: #333;">fai_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">read_fasta_index</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fai"</span><span class="p">)</span></span>

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

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<pre style="margin: 0;"> <span id="LC234" 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;">fai_lengths</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="322" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="320" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -322,7 +320,7 @@ def main():</td>

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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="323" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="321" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># compute base composition for genomic regions</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC322" class="line" lang="python">        <span class="n" style="color: #333;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">composition</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">count_ref_comp</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">before</span><span class="p">,</span> <span class="n" style="color: #333;">after</span><span class="p">,</span> <span class="n" style="color: #333;">dnacomp</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="python"><span class="idiff left right">        </span></span>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="324" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fasta</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="327" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="325" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python">            <span class="n" style="color: #333;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write_fasta</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">refseq</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">coordinate</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">coordinate</span><span class="p">),</span> <span class="n" style="color: #333;">before</span><span class="p">,</span> <span class="n" style="color: #333;">after</span><span class="p">,</span> <span class="n" style="color: #333;">fhfasta</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); 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="355" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -357,7 +355,7 @@ def main():</td>

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<td class="diff-line-num new_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tables</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_table_and_warn_if_dmg_freq_is_low</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="p">):</span></span>

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<td class="diff-line-num old_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="python">        <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">no_stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span></span>

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

</pre>

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<pre style="margin: 0;">-<span id="LC360" class="line" lang="python"><span class="idiff left right">   </span></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># run the Bayesian estimation</span></span>

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<td class="diff-line-num old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

362

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<pre style="margin: 0;"> <span id="LC360" 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;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">no_stats</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># before running the Bayesian estimation get the base composition</span></span>

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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">mapdamage (2.<span class="idiff left right">0.9+dfsg-2</span>) UNRELEASED; urgency=medium</span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mapdamage (2.<span class="idiff left right">1.0+dfsg-1</span>) 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">  * <span class="idiff left right">Use 2to3 to port to Python3</span></span>

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

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">    Closes: #936989</span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">  * debhelper-compat 12</span>

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">  * Standards-Version: 4.4.0</span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ mapdamage (2.0.9+dfsg-2) UNRELEASED; urgency=medium</td>

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

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * python3-pysam <!nocheck></span>

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Tue, 0<span class="idiff left right">3 Sep 2019 11:02:34</span> +0200</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Tue, 0<span class="idiff left right">1 Oct 2019 17:13:12</span> +0200</span>

</pre>

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

</pre>

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13

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

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">mapdamage (2.0.9+dfsg-1) unstable; urgency=medium</span>

</pre>

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

14

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

14

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

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="555c85016bd79aa8bbb523506af81b69d9c69534">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#555c85016bd79aa8bbb523506af81b69d9c69534"><strong>debian/patches/2to3.patch</strong>

deleted

</a>

<hr>

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

1

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<td class="diff-line-num new_line old" data-linenumber="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="diff"><span class="p">Description: Use 2to3 to port to Python3</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/936989</span></span>

</pre>

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

3

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

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>

</pre>

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4

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: Tue, 03 Sep 2019 11:02:34 +0200</span></span>

</pre>

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

</pre>

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6

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/bin/mapDamage</span>

</pre>

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

7

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/mapDamage</span></span>

</pre>

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

8

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

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>

</pre>

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

9

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

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/python</span></span>

</pre>

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10

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

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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11

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>

</pre>

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

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

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

</pre>

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

13

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

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from __future__ import print_function</span></span>

</pre>

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14

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

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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

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<td class="diff-line-num new_line old" data-linenumber="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="LC15" class="line" lang="diff"> </span>

</pre>

</td>

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

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

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> import logging</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -45,7 +45,7 @@</span> MODULE = "pysam"</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> URL = "http://code.google.com/p/pysam/"</span>

</pre>

</td>

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

20

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

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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="LC20" class="line" lang="diff"> try:</span>

</pre>

</td>

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

21

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

</td>

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

<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff">     __import__(MODULE)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

22

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<td class="diff-line-num new_line old" data-linenumber="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="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-except ImportError, e:</span></span>

</pre>

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

23

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

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except ImportError as e:</span></span>

</pre>

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

24

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<td class="diff-line-num new_line old" data-linenumber="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="LC24" class="line" lang="diff">     sys.stderr.write("Error: Could not import required module '%s':\n\t- %s\n" % (MODULE, e))</span>

</pre>

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

25

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

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff">     sys.stderr.write("       If module is not installed, please download from '%s'.\n" % URL)</span>

</pre>

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

26

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

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff">     sys.stderr.write("       A local install may be performed using the following command:\n")</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

27

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

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="p">@@ -98,7 +98,7 @@</span> def _downsample_to_fixed_number(bamfile,</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

28

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

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff">             if index >= downsample_to:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

29

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<td class="diff-line-num new_line old" data-linenumber="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="LC29" class="line" lang="diff">                 continue</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

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

</td>

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

<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff">         sample[index] = record</span>

</pre>

</td>

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

31

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

</td>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    return filter(None, sample)</span></span>

</pre>

</td>

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

32

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

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    return [_f for _f in sample if _f]</span></span>

</pre>

</td>

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

33

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

</td>

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

<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> </span>

</pre>

</td>

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

34

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

</td>

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

<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

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

35

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

</td>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"> def _read_bamfile(bamfile, options):</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

36

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

</td>

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="p">@@ -121,7 +121,7 @@</span> def _check_mm_option():</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

37

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

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff">     in mapdamage.parseoptions</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

38

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

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

</pre>

</td>

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

39

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

</td>

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

<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff">     path_to_mm = None</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

40

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

</td>

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

<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for nr,arg in zip(xrange(len(sys.argv)),sys.argv):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

41

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

</td>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for nr,arg in zip(range(len(sys.argv)),sys.argv):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

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

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff">         if arg.startswith("--mapdamage-modules"):</span>

</pre>

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

43

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

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff">             try:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

44

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

</td>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff">                 if "=" in arg:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

45

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

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="p">@@ -230,7 +230,7 @@</span> def main():</span>

</pre>

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

46

</td>

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

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff">         in_bam = pysam.Samfile(options.filename)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

47

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

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

48

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

</td>

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

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

49

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

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    reflengths = dict(zip(in_bam.references, in_bam.lengths))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

50

</td>

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

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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="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    reflengths = dict(list(zip(in_bam.references, in_bam.lengths)))</span></span>

</pre>

</td>

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

51

</td>

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

</td>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff">     # check if references in SAM/BAM are the same in the fasta reference file</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

52

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<td class="diff-line-num new_line old" data-linenumber="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="LC52" class="line" lang="diff">     fai_lengths = mapdamage.seq.read_fasta_index(options.ref + ".fai")</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

53

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<td class="diff-line-num new_line old" data-linenumber="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="LC53" class="line" lang="diff">     if not fai_lengths:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

54

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

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/__init__.py</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

55

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<td class="diff-line-num new_line old" data-linenumber="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="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/__init__.py</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

56

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<td class="diff-line-num new_line old" data-linenumber="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="LC56" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

57

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<td class="diff-line-num new_line old" data-linenumber="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="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

58

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<td class="diff-line-num new_line old" data-linenumber="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="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

59

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<td class="diff-line-num new_line old" data-linenumber="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="LC59" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

60

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<td class="diff-line-num new_line old" data-linenumber="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="LC60" class="line" lang="diff"> import mapdamage.parseoptions</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

61

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

</td>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"> import mapdamage.seq</span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/align.py</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/align.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"> import itertools</span>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"> import mapdamage</span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="p">@@ -84,7 +84,7 @@</span> def get_mis(read, seq, refseq, ref, leng</span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff">   std = '-' if read.is_reverse else '+'</span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff">   subtable = tab[ref][end][std]</span>

</pre>

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  for (i, nt_seq, nt_ref) in itertools.izip(xrange(length), seq, refseq):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  for (i, nt_seq, nt_ref) in zip(range(length), seq, refseq):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff">     if (nt_seq in "ACGT-") and (nt_ref in "ACGT-"):</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff">       if nt_ref != "-":</span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff">         # record base composition in the reference, only A, C, G, T</span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/composition.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/composition.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

</pre>

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83

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</td>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

84

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

85

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> import mapdamage</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"> import itertools</span>

</pre>

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

87

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

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="p">@@ -10,8 +10,8 @@</span> def count_ref_comp(read, chrom, before,</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff">   """ record basae composition in external genomic regions """</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

89

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

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff">   std = '-' if read.is_reverse else '+'</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(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="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  _update_table(comp[chrom]['5p'][std], before, xrange(-len(before), 0))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  _update_table(comp[chrom]['3p'][std], after,  xrange(1, len(after) + 1))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="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="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  _update_table(comp[chrom]['5p'][std], before, range(-len(before), 0))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  _update_table(comp[chrom]['3p'][std], after,  range(1, len(after) + 1))</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"> </span>

</pre>

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

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

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

</pre>

</td>

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

97

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

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"> def count_read_comp(read, chrom, length, comp):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

98

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

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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="p">@@ -20,12 +20,12 @@</span> def count_read_comp(read, chrom, length,</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

99

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

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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff">   if read.is_reverse:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff">     std, seq = '-', mapdamage.seq.revcomp(seq)</span>

</pre>

</td>

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

101

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<td class="diff-line-num new_line old" data-linenumber="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="LC101" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

102

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<pre style="margin: 0;">-<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  _update_table(comp[chrom]['5p'][std], seq,           xrange(1, length + 1))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  _update_table(comp[chrom]['3p'][std], reversed(seq), xrange(-1, - length - 1, -1))</span></span>

</pre>

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

104

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  _update_table(comp[chrom]['5p'][std], seq,           range(1, length + 1))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

105

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

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  _update_table(comp[chrom]['3p'][std], reversed(seq), range(-1, - length - 1, -1))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

106

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

107

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

108

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="diff"> def _update_table(table, sequence, indices):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="109" style="width: 35px; color: rgba(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="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  for (index, nt) in itertools.izip(indices, sequence):</span></span>

</pre>

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110

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  for (index, nt) in zip(indices, sequence):</span></span>

</pre>

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

111

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff">     if nt in table:</span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC112" class="line" lang="diff">       table[nt][index] += 1</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(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="LC113" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="114" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

114

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="p">@@ -47,7 +47,7 @@</span> def get_base_comp(filename,destination=F</span>

</pre>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff">             bases["C"] = bases["C"] + int(tabs[3])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="116" style="width: 35px; color: rgba(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="LC116" class="line" lang="diff">             bases["G"] = bases["G"] + int(tabs[4])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="117" style="width: 35px; color: rgba(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="LC117" class="line" lang="diff">             bases["T"] = bases["T"] + int(tabs[5])</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="118" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

118

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<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    except (OSError, ValueError), error:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="119" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    except (OSError, ValueError) as error:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

120

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff">         sys.stderr.write("Error: Seqtk failed: %s\n" % (error,))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="121" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

121

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<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff">         sys.exit(1)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="122" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

122

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff">     # get the base frequencies</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="123" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

123

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/parseoptions.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/parseoptions.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

128

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="129" style="width: 35px; color: rgba(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="LC129" class="line" lang="diff"> from optparse import OptionParser, OptionGroup, SUPPRESS_HELP</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="130" style="width: 35px; color: rgba(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="LC130" class="line" lang="diff"> import os</span>

</pre>

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<td class="diff-line-num old old_line" 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="diff"><span class="p">@@ -235,12 +235,12 @@</span> def options():</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

132

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

133

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff">     if os.path.isdir(options.folder):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="134" style="width: 35px; color: rgba(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="LC134" class="line" lang="diff">         if not options.quiet and not options.plot_only:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            print("Warning, %s already exists" % options.folder)</span></span>

</pre>

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136

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            print(("Warning, %s already exists" % options.folder))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(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="LC137" class="line" lang="diff">         if options.plot_only:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="138" style="width: 35px; color: rgba(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="LC138" class="line" lang="diff">             if not file_exist(options.folder+"/dnacomp.txt") or not file_exist(options.folder+"/misincorporation.txt"):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

139

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff">                 parser.error('folder %s is not a valid result folder' % options.folder)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff">     else:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

141

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        os.makedirs(options.folder, mode = 0750)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

142

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

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        os.makedirs(options.folder, mode = 0o750)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

143

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

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff">         if options.plot_only or options.stats_only or options.rescale_only:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

144

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

</td>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff">             sys.stderr.write("Error, %s does not exist while plot/stats/rescale only was used\n" % options.folder)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="145" style="width: 35px; color: rgba(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="LC145" class="line" lang="diff">             return None</span>

</pre>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/rescale.py</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="147" style="width: 35px; color: rgba(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="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/rescale.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="p">@@ -31,14 +31,14 @@</span> def get_corr_prob(folder, rescale_length</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC149" class="line" lang="diff">         fi_handle = csv.DictReader(open(full_path))</span>

</pre>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff">         corr_prob = {}</span>

</pre>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff">         for line in fi_handle:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if (corr_prob.has_key(line["Position"])):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            if (line["Position"] in corr_prob):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff">                 sys.exit('This file has multiple position definitions %s, line %d: %s' % \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff">                     (folder, fi_handle.line_num, corr_prob[line["Position"]]))</span>

</pre>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff">             else:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff">                 corr_prob[int(line["Position"])] = {'C.T':float(line["C.T"]), 'G.A':float(line["G.A"])}</span>

</pre>

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<pre style="margin: 0;">-<span id="LC158" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff">         # Exclude probabilities for positions outside of user-specified region</span>

</pre>

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<pre style="margin: 0;">-<span id="LC160" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for key in corr_prob.keys():</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        for key in list(corr_prob.keys()):</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="LC162" class="line" lang="diff">             if key < -rescale_length_3p or key > rescale_length_5p:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff">                 corr_prob.pop(key)</span>

</pre>

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<td class="diff-line-num old old_line" 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="LC164" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"><span class="p">@@ -75,13 +75,13 @@</span> def corr_this_base(corr_prob, nt_seq, nt</span>

</pre>

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff">     back_pos = pos-length-1 </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

167

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="diff">     # position from 3' end</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

168

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

169

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    if corr_prob.has_key(pos):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

170

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<pre style="margin: 0;">-<span id="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if pos in corr_prob:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="171" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

171

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff">         p5_corr = corr_prob[pos][subs]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="172" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

172

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff">         # correction from 5' end</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

173

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff">     else:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

174

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff">         p5_corr = 0</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

175

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

176

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    if corr_prob.has_key(back_pos):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

177

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    if back_pos in corr_prob:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

178

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff">         p3_corr = corr_prob[back_pos][subs]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

179

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff">         # correction from 3' end</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

180

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="diff">     else:</span>

</pre>

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

181

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="p">@@ -104,7 +104,7 @@</span> def corr_this_base(corr_prob, nt_seq, nt</span>

</pre>

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

182

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<pre style="margin: 0;">-<span id="LC182" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="183" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

183

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"> def initialize_subs():</span>

</pre>

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

184

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<pre style="margin: 0;">-<span id="LC184" class="line" lang="diff">     """Initialize a substitution table, to track the expected substitution counts"""</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

185

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    per_qual = dict(zip(range(0,130),[0]*130))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

186

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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    per_qual = dict(list(zip(list(range(0,130)),[0]*130)))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

187

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<pre style="margin: 0;">-<span id="LC187" class="line" lang="diff">     subs = {"CT-before":per_qual.copy(),\</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

188

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

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff">             "TC-before":per_qual.copy(),\</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

189

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

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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff">             "GA-before":per_qual.copy(),\</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

190

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

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="p">@@ -164,7 +164,7 @@</span> def qual_summary_subs(subs):</span>

</pre>

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

191

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

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<pre style="margin: 0;">-<span id="LC191" class="line" lang="diff">             for qv in subs[i]:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

192

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

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<pre style="margin: 0;">-<span id="LC192" class="line" lang="diff">                 if qv >= lv :</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

193

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

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<pre style="margin: 0;">-<span id="LC193" class="line" lang="diff">                     key = i+"-Q"+str(lv)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

194

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                    if subs.has_key(key):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

195

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

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<pre style="margin: 0;">-<span id="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                    if key in subs:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

196

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

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff">                         subs[key] += subs[i][qv]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

197

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

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

</pre>

</td>

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

198

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff">                         subs[key] = subs[i][qv]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

199

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

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<pre style="margin: 0;">-<span id="LC199" class="line" lang="diff"><span class="p">@@ -174,32 +174,32 @@</span> def print_subs(subs):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

200

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

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="diff">     print("\tThe expected substition frequencies before and after scaling using the scaled qualities as probalities:")</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

201

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

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<pre style="margin: 0;">-<span id="LC201" class="line" lang="diff">     if subs["C"]!=0:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

202

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

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="diff">         # the special case of no substitutions</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

203

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

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<pre style="margin: 0;">-<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print("\tCT\t"+str(subs["CT-pvals_before"]/subs["C"])+"\t\t"+str(subs["CT-pvals"]/subs["C"]))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

204

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

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<pre style="margin: 0;">-<span id="LC204" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print(("\tCT\t"+str(subs["CT-pvals_before"]/subs["C"])+"\t\t"+str(subs["CT-pvals"]/subs["C"])))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

205

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

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="206" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

206

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

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff">         print("\tCT\tNA\t\tNA")</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="207" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

207

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff">     if subs["T"]!=0:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="208" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

208

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

</td>

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

<pre style="margin: 0;">-<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print("\tTC\t"+str(subs["TC-pvals"]/subs["T"])+"\t\t"+str(subs["TC-pvals"]/subs["T"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="209" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

209

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print(("\tTC\t"+str(subs["TC-pvals"]/subs["T"])+"\t\t"+str(subs["TC-pvals"]/subs["T"])))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

210

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff">     else:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

211

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff">         print("\tTC\tNA\t\tNA")</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="212" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

212

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC212" class="line" lang="diff">     if subs["G"]!=0:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="213" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

213

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print("\tGA\t"+str(subs["GA-pvals_before"]/subs["G"])+"\t\t"+str(subs["GA-pvals"]/subs["G"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="214" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

214

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC214" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print(("\tGA\t"+str(subs["GA-pvals_before"]/subs["G"])+"\t\t"+str(subs["GA-pvals"]/subs["G"])))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

215

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC215" class="line" lang="diff">     else:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="216" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

216

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC216" class="line" lang="diff">         print("\tGA\tNA\t\tNA")</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="217" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

217

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC217" class="line" lang="diff">     if subs["A"]!=0:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="218" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

218

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print("\tAG\t"+str(subs["AG-pvals"]/subs["A"])+"\t\t"+str(subs["AG-pvals"]/subs["A"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="219" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

219

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC219" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print(("\tAG\t"+str(subs["AG-pvals"]/subs["A"])+"\t\t"+str(subs["AG-pvals"]/subs["A"])))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="220" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

220

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC220" class="line" lang="diff">     else:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="221" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

221

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC221" class="line" lang="diff">         print("\tAG\tNA\t\tNA")</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

222

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC222" class="line" lang="diff">     print("\tQuality metrics before and after scaling")</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

223

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tCT-Q0 \t"+str(subs["CT-before-Q0"])+"\t\t"+str(subs["CT-after-Q0"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

224

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tCT-Q10 \t"+str(subs["CT-before-Q10"])+"\t\t"+str(subs["CT-after-Q10"]))</span></span>

</pre>

</td>

</tr>

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

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

225

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tCT-Q20 \t"+str(subs["CT-before-Q20"])+"\t\t"+str(subs["CT-after-Q20"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="226" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

226

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tCT-Q30 \t"+str(subs["CT-before-Q30"])+"\t\t"+str(subs["CT-after-Q30"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="227" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

227

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC227" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tCT-Q40 \t"+str(subs["CT-before-Q40"])+"\t\t"+str(subs["CT-after-Q40"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="228" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

228

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC228" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tGA-Q0 \t"+str(subs["GA-before-Q0"])+"\t\t"+str(subs["GA-after-Q0"]))</span></span>

</pre>

</td>

</tr>

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

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

229

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC229" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tGA-Q10 \t"+str(subs["GA-before-Q10"])+"\t\t"+str(subs["GA-after-Q10"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="230" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

230

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC230" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tGA-Q20 \t"+str(subs["GA-before-Q20"])+"\t\t"+str(subs["GA-after-Q20"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="231" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

231

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC231" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tGA-Q30 \t"+str(subs["GA-before-Q30"])+"\t\t"+str(subs["GA-after-Q30"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="232" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

232

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC232" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("\tGA-Q40 \t"+str(subs["GA-before-Q40"])+"\t\t"+str(subs["GA-after-Q40"]))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

233

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tCT-Q0 \t"+str(subs["CT-before-Q0"])+"\t\t"+str(subs["CT-after-Q0"])))</span></span>

</pre>

</td>

</tr>

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

234

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tCT-Q10 \t"+str(subs["CT-before-Q10"])+"\t\t"+str(subs["CT-after-Q10"])))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

235

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC235" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tCT-Q20 \t"+str(subs["CT-before-Q20"])+"\t\t"+str(subs["CT-after-Q20"])))</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

236

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tCT-Q30 \t"+str(subs["CT-before-Q30"])+"\t\t"+str(subs["CT-after-Q30"])))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

237

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tCT-Q40 \t"+str(subs["CT-before-Q40"])+"\t\t"+str(subs["CT-after-Q40"])))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

238

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tGA-Q0 \t"+str(subs["GA-before-Q0"])+"\t\t"+str(subs["GA-after-Q0"])))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

239

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tGA-Q10 \t"+str(subs["GA-before-Q10"])+"\t\t"+str(subs["GA-after-Q10"])))</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

240

</td>

<td class="diff-line-num new_line old" data-linenumber="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="LC240" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tGA-Q20 \t"+str(subs["GA-before-Q20"])+"\t\t"+str(subs["GA-after-Q20"])))</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

241

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tGA-Q30 \t"+str(subs["GA-before-Q30"])+"\t\t"+str(subs["GA-after-Q30"])))</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num old old_line" data-linenumber="242" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

242

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("\tGA-Q40 \t"+str(subs["GA-before-Q40"])+"\t\t"+str(subs["GA-after-Q40"])))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="243" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

243

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC243" class="line" lang="diff">     </span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

244

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

</td>

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

<pre style="margin: 0;">-<span id="LC244" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</td>

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

<pre style="margin: 0;">-<span id="LC245" class="line" lang="diff"> def rescale_qual_read(bam, read, ref, corr_prob,subs, debug = False,direction="both"):</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

246

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

</td>

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

<pre style="margin: 0;">-<span id="LC246" class="line" lang="diff"><span class="p">@@ -237,7 +237,7 @@</span> def rescale_qual_read(bam, read, ref, co</span>

</pre>

</td>

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

247

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<td class="diff-line-num new_line old" data-linenumber="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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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC247" class="line" lang="diff">     new_qual = [-100]*length_read</span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC248" class="line" lang="diff">     pos_on_read = 0</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="249" style="width: 35px; color: rgba(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="LC249" class="line" lang="diff">     number_of_rescaled_bases = 0.0</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="250" style="width: 35px; color: rgba(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="LC250" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for (i, nt_seq, nt_ref, nt_qual) in itertools.izip(xrange(length_align), seq, refseq, qual):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="251" style="width: 35px; color: rgba(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="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for (i, nt_seq, nt_ref, nt_qual) in zip(range(length_align), seq, refseq, qual):</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC252" class="line" lang="diff">         # rescale the quality according to the triplet position, </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="253" style="width: 35px; color: rgba(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="LC253" class="line" lang="diff">         # pair of the reference and the sequence</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="254" style="width: 35px; color: rgba(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="LC254" class="line" lang="diff">         if ((nt_seq == "T" and nt_ref =="C") or (nt_seq == "A" and nt_ref =="G")):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC255" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/rescale_test.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/rescale_test.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC257" class="line" lang="diff"><span class="p">@@ -1,6 +1,9 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC258" class="line" lang="diff"> import unittest</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC259" class="line" lang="diff"> import optparse</span>

</pre>

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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import rescale</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+try:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    from . import rescale</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="263" style="width: 35px; color: rgba(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="LC263" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+except:</span></span>

</pre>

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<td class="diff-line-num old old_line" 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="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    from mapdamage import rescale</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="265" style="width: 35px; color: rgba(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="LC265" class="line" lang="diff"> import pysam</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="266" style="width: 35px; color: rgba(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="LC266" class="line" lang="diff"> import filecmp</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="267" style="width: 35px; color: rgba(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="LC267" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="268" style="width: 35px; color: rgba(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="LC268" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/rscript.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/rscript.py</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC271" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC272" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC273" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(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="LC274" class="line" lang="diff"> import os</span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC275" class="line" lang="diff"> import subprocess</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="276" style="width: 35px; color: rgba(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="LC276" class="line" lang="diff"><span class="p">@@ -35,11 +35,11 @@</span> def plot(opt):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC277" class="line" lang="diff">   script = construct_path("mapDamage.R") </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="278" style="width: 35px; color: rgba(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="LC278" class="line" lang="diff">   call = ["Rscript", script, fcomp, title, opt.refplot, fmut, opt.readplot, \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC279" class="line" lang="diff">       opt.ymax, opt.folder, opt.title, __version__]</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="280" style="width: 35px; color: rgba(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="LC280" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  code = subprocess.call(map(str, call))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  code = subprocess.call(list(map(str, call)))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</td>

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<pre style="margin: 0;">-<span id="LC283" class="line" lang="diff">   if code == 0:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

284

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

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<pre style="margin: 0;">-<span id="LC284" class="line" lang="diff">     if not opt.quiet:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</td>

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<pre style="margin: 0;">-<span id="LC285" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      print("pdf %s generated" % title)</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

286

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

</td>

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

<pre style="margin: 0;">-<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      print(("pdf %s generated" % title))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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<pre style="margin: 0;">-<span id="LC287" class="line" lang="diff">     return 0</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

288

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

</td>

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

</td>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="diff">     print("Error: plotting with R failed")</span>

</pre>

</td>

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<pre style="margin: 0;">-<span id="LC290" class="line" lang="diff"><span class="p">@@ -58,7 +58,7 @@</span> def opt_plots(opt):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC291" class="line" lang="diff">   script = construct_path("lengths.R") </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="292" style="width: 35px; color: rgba(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="LC292" class="line" lang="diff">   call = ["Rscript", script, flength, output, fmut, opt.length, \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC293" class="line" lang="diff">       opt.title, __version__, bool_to_int(opt.quiet)]</span>

</pre>

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<pre style="margin: 0;">-<span id="LC294" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  code = subprocess.call(map(str, call))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC295" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  code = subprocess.call(list(map(str, call)))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC296" class="line" lang="diff">   if code == 0:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC297" class="line" lang="diff">     return 0</span>

</pre>

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<pre style="margin: 0;">-<span id="LC298" class="line" lang="diff">   else:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="299" style="width: 35px; color: rgba(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="LC299" class="line" lang="diff"><span class="p">@@ -90,11 +90,11 @@</span> def check_R_lib():</span>

</pre>

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<pre style="margin: 0;">-<span id="LC300" class="line" lang="diff">     if len(missing_lib) > 1:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC301" class="line" lang="diff">         # Grammar Nazi has arrived</span>

</pre>

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<pre style="margin: 0;">-<span id="LC302" class="line" lang="diff">         last_ele = missing_lib.pop()</span>

</pre>

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<pre style="margin: 0;">-<span id="LC303" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print ("Missing the following R libraries '" + "', '".join(missing_lib) \</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC304" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            + "' and '" + last_ele + "'")</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print(("Missing the following R libraries '" + "', '".join(missing_lib) \</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC306" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            + "' and '" + last_ele + "'"))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="307" style="width: 35px; color: rgba(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="LC307" class="line" lang="diff">         return 1</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="308" style="width: 35px; color: rgba(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="LC308" class="line" lang="diff">     elif len(missing_lib) == 1:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="309" style="width: 35px; color: rgba(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="LC309" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print ("Missing the following R library "+missing_lib[0])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="310" style="width: 35px; color: rgba(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="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print(("Missing the following R library "+missing_lib[0]))</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC311" class="line" lang="diff">         return 1</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="312" style="width: 35px; color: rgba(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="LC312" class="line" lang="diff">     else :</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="313" style="width: 35px; color: rgba(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="LC313" class="line" lang="diff">         # No missing libraries</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="314" style="width: 35px; color: rgba(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="LC314" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/seq.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC315" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/seq.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC316" class="line" lang="diff"><span class="p">@@ -1,9 +1,9 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC317" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC319" class="line" lang="diff"> import sys</span>

</pre>

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<pre style="margin: 0;">-<span id="LC320" class="line" lang="diff"> import string</span>

</pre>

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<pre style="margin: 0;">-<span id="LC321" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="322" style="width: 35px; color: rgba(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="LC322" class="line" lang="diff"> # from Martin Kircher, to complement DNA</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="323" style="width: 35px; color: rgba(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="LC323" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-TABLE = string.maketrans('TGCAMRWSYKVHDBtgcamrwsykvhdb', \</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC324" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+TABLE = str.maketrans('TGCAMRWSYKVHDBtgcamrwsykvhdb', \</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC325" class="line" lang="diff">     'ACGTKYWSRMBDHVacgtkywsrmbdhv')</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="326" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

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

<pre style="margin: 0;">-<span id="LC326" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="327" style="width: 35px; color: rgba(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="LC327" class="line" lang="diff"> LETTERS = ("A", "C", "G", "T")</span>

</pre>

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<pre style="margin: 0;">-<span id="LC328" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/tables.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/tables.py</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC330" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC331" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC332" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

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<pre style="margin: 0;">-<span id="LC333" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC334" class="line" lang="diff"> import os</span>

</pre>

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<pre style="margin: 0;">-<span id="LC335" class="line" lang="diff"> import collections</span>

</pre>

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="diff"><span class="p">@@ -16,7 +16,7 @@</span> def initialize_mut(ref, length):</span>

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<pre style="margin: 0;">-<span id="LC337" class="line" lang="diff">       for std in ('+','-'):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC338" class="line" lang="diff">         tab_std = tab_end[std] = {}</span>

</pre>

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<pre style="margin: 0;">-<span id="LC339" class="line" lang="diff">         for mut in mapdamage.seq.HEADER:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC340" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          tab_std[mut] = dict.fromkeys(xrange(length), 0)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC341" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          tab_std[mut] = dict.fromkeys(range(length), 0)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC342" class="line" lang="diff">   </span>

</pre>

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<pre style="margin: 0;">-<span id="LC343" class="line" lang="diff">   return tab</span>

</pre>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="diff"><span class="p">@@ -26,8 +26,8 @@</span> def print_mut(mut, opt, out):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC346" class="line" lang="diff"> </span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC348" class="line" lang="diff"> def initialize_comp(ref, around, length):</span>

</pre>

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<pre style="margin: 0;">-<span id="LC349" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  keys = {"3p" : range(-length, 0) + range(1, around + 1),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-          "5p" : range(-around, 0) + range(1, length + 1)}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  keys = {"3p" : list(range(-length, 0)) + list(range(1, around + 1)),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC352" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          "5p" : list(range(-around, 0)) + list(range(1, length + 1))}</span></span>

</pre>

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353

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<pre style="margin: 0;">-<span id="LC353" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="354" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

354

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

</td>

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<pre style="margin: 0;">-<span id="LC354" class="line" lang="diff">   tab = {}</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

355

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

</td>

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<pre style="margin: 0;">-<span id="LC355" class="line" lang="diff">   for contig in ref:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="356" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

356

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

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<pre style="margin: 0;">-<span id="LC356" class="line" lang="diff"><span class="p">@@ -74,8 +74,8 @@</span> def check_table_and_warn_if_dmg_freq_is_</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="357" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

357

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

</td>

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

<pre style="margin: 0;">-<span id="LC357" class="line" lang="diff">   total = 0.0</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="358" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

358

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

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

<pre style="margin: 0;">-<span id="LC358" class="line" lang="diff">   for filename in ("5pCtoT_freq.txt", "3pGtoA_freq.txt"):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="359" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

359

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

</td>

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

<pre style="margin: 0;">-<span id="LC359" class="line" lang="diff">     if not os.path.exists(folder+"/"+filename):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="360" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

360

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

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

<pre style="margin: 0;">-<span id="LC360" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      print("Error: Required table has not been created ('%s'), bayesian computation cannot be performed" \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="361" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

361

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

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<pre style="margin: 0;">-<span id="LC361" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            % filename)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="362" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

362

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

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<pre style="margin: 0;">-<span id="LC362" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      print(("Error: Required table has not been created ('%s'), bayesian computation cannot be performed" \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

363

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

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<pre style="margin: 0;">-<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            % filename))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="364" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

364

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

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<pre style="margin: 0;">-<span id="LC364" class="line" lang="diff">       return True</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="365" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

365

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

</td>

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

<pre style="margin: 0;">-<span id="LC365" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="366" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

366

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

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

<pre style="margin: 0;">-<span id="LC366" class="line" lang="diff">     with open(os.path.join(folder, filename)) as handle:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="367" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

367

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

</td>

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

<pre style="margin: 0;">-<span id="LC367" class="line" lang="diff"><span class="p">@@ -85,12 +85,12 @@</span> def check_table_and_warn_if_dmg_freq_is_</span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="368" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

368

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<td class="diff-line-num new_line old" data-linenumber="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="LC368" class="line" lang="diff">           total += float(freq[1])</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="369" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

369

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

</td>

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

<pre style="margin: 0;">-<span id="LC369" class="line" lang="diff">           break</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="370" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

370

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

</td>

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

<pre style="margin: 0;">-<span id="LC370" class="line" lang="diff">       else:</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="371" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

371

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

</td>

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

<pre style="margin: 0;">-<span id="LC371" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        print("Error: Could not find pos = 1 in table '%s', bayesian computation cannot be performed" \</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="372" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

372

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

</td>

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

<pre style="margin: 0;">-<span id="LC372" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-              % filename)</span></span>

</pre>

</td>

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

<td class="diff-line-num old old_line" data-linenumber="373" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

373

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

</td>

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

<pre style="margin: 0;">-<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        print(("Error: Could not find pos = 1 in table '%s', bayesian computation cannot be performed" \</span></span>

</pre>

</td>

</tr>

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374

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

</td>

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<pre style="margin: 0;">-<span id="LC374" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+              % filename))</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

375

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

</td>

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<pre style="margin: 0;">-<span id="LC375" class="line" lang="diff">         return True</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="376" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

376

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

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

<pre style="margin: 0;">-<span id="LC376" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="377" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

377

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

</td>

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

<pre style="margin: 0;">-<span id="LC377" class="line" lang="diff">   if total < 0.01:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="378" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

378

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

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<pre style="margin: 0;">-<span id="LC378" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    print("Warning: DNA damage levels are too low, the Bayesian computation should not be performed (%f < 0.01)\n" % total)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="379" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

379

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

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<pre style="margin: 0;">-<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    print(("Warning: DNA damage levels are too low, the Bayesian computation should not be performed (%f < 0.01)\n" % total))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="380" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

380

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

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

<pre style="margin: 0;">-<span id="LC380" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

381

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

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<pre style="margin: 0;">-<span id="LC381" class="line" lang="diff">   return False</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="382" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

382

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

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

<pre style="margin: 0;">-<span id="LC382" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="383" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

383

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

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<pre style="margin: 0;">-<span id="LC383" class="line" lang="diff"><span class="p">@@ -103,9 +103,9 @@</span> def _print_freq_table(table, columns, op</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="384" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

384

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

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<pre style="margin: 0;">-<span id="LC384" class="line" lang="diff">   out.write("# Chr: reference from sam/bam header, End: from which termini of DNA sequences, Std: strand of reads\n")</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="385" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

385

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

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<pre style="margin: 0;">-<span id="LC385" class="line" lang="diff">   out.write("Chr\tEnd\tStd\tPos\t%s\n" % ("\t".join(columns)))</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="386" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

386

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

</td>

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

<pre style="margin: 0;">-<span id="LC386" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

387

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

</td>

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

<pre style="margin: 0;">-<span id="LC387" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  for (reference, ends) in sorted(table.iteritems()):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

388

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

</td>

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

<pre style="margin: 0;">-<span id="LC388" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    for (end, strands) in sorted(ends.iteritems()):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

389

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

</td>

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

<pre style="margin: 0;">-<span id="LC389" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-      for (strand, subtable) in sorted(strands.iteritems()):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

390

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC390" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  for (reference, ends) in sorted(table.items()):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="391" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

391

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

</td>

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

<pre style="margin: 0;">-<span id="LC391" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for (end, strands) in sorted(ends.items()):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="392" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

392

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      for (strand, subtable) in sorted(strands.items()):</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="393" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

393

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

</td>

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<pre style="margin: 0;">-<span id="LC393" class="line" lang="diff">         subtable["Total"] = {}</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="394" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

394

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

</td>

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

<pre style="margin: 0;">-<span id="LC394" class="line" lang="diff">         for index in sorted(subtable[columns[0]]):</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="395" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

395

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

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

<pre style="margin: 0;">-<span id="LC395" class="line" lang="diff">           subtable["Total"][index] = sum(subtable[letter][index] for letter in mapdamage.seq.LETTERS)</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="396" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

396

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

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<pre style="margin: 0;">-<span id="LC396" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/version.py</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="397" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

397

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

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<pre style="margin: 0;">-<span id="LC397" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/version.py</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="398" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

398

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

</td>

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<pre style="margin: 0;">-<span id="LC398" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="399" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

399

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

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<pre style="margin: 0;">-<span id="LC399" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

</pre>

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400

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

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<pre style="margin: 0;">-<span id="LC400" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="401" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

401

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

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<pre style="margin: 0;">-<span id="LC401" class="line" lang="diff"> try:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="402" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

402

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

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<pre style="margin: 0;">-<span id="LC402" class="line" lang="diff">     from mapdamage._version import __version__</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="403" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

403

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

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<pre style="margin: 0;">-<span id="LC403" class="line" lang="diff"> except ImportError:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="404" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

404

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

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<pre style="margin: 0;">-<span id="LC404" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/setup.py</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="405" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

405

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

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

<pre style="margin: 0;">-<span id="LC405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="406" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

406

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

</td>

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<pre style="margin: 0;">-<span id="LC406" class="line" lang="diff"><span class="p">@@ -1,4 +1,4 @@</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="407" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

407

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

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<pre style="margin: 0;">-<span id="LC407" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-#!/usr/bin/env python</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="408" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

408

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

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<pre style="margin: 0;">-<span id="LC408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#!/usr/bin/python3</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="409" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

409

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

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

<pre style="margin: 0;">-<span id="LC409" class="line" lang="diff"> # -*- coding: utf-8 -*-</span>

</pre>

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

410

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

</td>

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

<pre style="margin: 0;">-<span id="LC410" class="line" lang="diff"> </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="411" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

411

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

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<pre style="margin: 0;">-<span id="LC411" class="line" lang="diff"> from distutils.core import setup</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="412" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

412

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

</td>

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

<pre style="margin: 0;">-<span id="LC412" class="line" lang="diff"><span class="p">@@ -14,9 +14,9 @@</span> def setup_version():</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="413" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

413

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

</td>

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

<pre style="margin: 0;">-<span id="LC413" class="line" lang="diff">     try:</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="414" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

414

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

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<pre style="margin: 0;">-<span id="LC414" class="line" lang="diff">         version = subprocess.check_output(("git", "describe", "--always", "--tags", "--dirty"))</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="415" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

415

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

</td>

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<pre style="margin: 0;">-<span id="LC415" class="line" lang="diff">         with open(os.path.join("mapdamage", "_version.py"), "w") as handle:</span>

</pre>

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<pre style="margin: 0;">-<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            handle.write("#!/usr/bin/env python\n")</span></span>

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<pre style="margin: 0;">-<span id="LC417" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+            handle.write("#!/usr/bin/python3\n")</span></span>

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<pre style="margin: 0;">-<span id="LC418" class="line" lang="diff">             handle.write("__version__ = %r\n" % (version.strip(),))</span>

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<pre style="margin: 0;">-<span id="LC419" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    except (subprocess.CalledProcessError, OSError), error:</span></span>

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<pre style="margin: 0;">-<span id="LC420" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    except (subprocess.CalledProcessError, OSError) as error:</span></span>

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<pre style="margin: 0;">-<span id="LC421" class="line" lang="diff">         raise SystemExit("Could not determine mapDamage version: %s" % (error,))</span>

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<pre style="margin: 0;">-<span id="LC422" class="line" lang="diff"> </span>

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<pre style="margin: 0;">-<span id="LC423" class="line" lang="diff"> </span></pre>

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<br>

</li>

<li id="88645f50aec6faa6b6917074e6c75473dad1acb5">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#88645f50aec6faa6b6917074e6c75473dad1acb5"><strong>debian/patches/fix_quantile_na_rm.patch</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,11 +4,9 @@ Description: change calcSampleStats such as any NA and Nan's are</td>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2017-03-28</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="p">Bug: https://github.com/ginolhac/mapDamage/issues/18</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">Index: mapdamage/mapdamage/Rscripts/stats/function.R</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mapdamage.orig/mapdamage/Rscripts/stats/function.R     2017-03-29 00:02:46.538470957 -0400</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mapdamage/mapdamage/Rscripts/stats/function.R 2017-03-29 00:11:09.141025051 -0400</span></span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -595,8 +595,8 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/mapdamage/Rscripts/stats/function.R</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/Rscripts/stats/function.R</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -595,8 +595,8 @@</span> calcSampleStats <- function(da,X){</span>

</pre>

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10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff">                       pos=da[,"Pos"],</span>

</pre>

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

13

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

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff">                       mea=apply(X,1,mean),</span>

</pre>

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

14

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

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff">                       med=apply(X,1,median),</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

<hr>

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

1

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

1

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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

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

3

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

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">2to3.patch</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="04da551d7b8b96ce0f039c05c3a01a8f3590d1a0">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#04da551d7b8b96ce0f039c05c3a01a8f3590d1a0"><strong>debian/patches/use_debian_packaged_seqtk.patch</strong></a>

<hr>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,23 +27,24 @@ Description: Use Debian packaged seqtk</td>

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

27

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27

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> def setup_version():</span>

</pre>

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

28

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28

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff">     if not os.path.exists(".git"):</span>

</pre>

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

29

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

29

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff">         # Release version, no .git folder</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

30

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<td class="diff-line-num new_line old" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="p">@@ -40,1<span class="idiff left right">6 +25,7</span> @@</span> class compileInstall(DistutilsInstall):</span>

</pre>

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

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<td class="diff-line-num new new_line" 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="diff"><span class="p">@@ -40,1<span class="idiff left right">7 +25,8</span> @@</span> class compileInstall(DistutilsInstall):</span>

</pre>

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

31

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

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff">     def run(self):</span>

</pre>

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

32

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

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff">         self.record=""</span>

</pre>

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

33

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

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff">         setup_version()</span>

</pre>

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

34

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

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        compile_seqtk()</span></span>

</pre>

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

35

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff">         DistutilsInstall.run(self)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

36

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<td class="diff-line-num new_line old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;"><span class="idiff left right">-</span>        # fixing the permission problem of seqtk</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

36

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="idiff left right"> </span>        # fixing the permission problem of seqtk</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        files = self.get_outputs()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-        for fi in files:</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-            if fi.endswith("seqtk/seqtk"):</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                os.chmod(fi,0755)</span></span>

</pre>

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<td class="diff-line-num new old_line" 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="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                os.chmod(fi,0o755)</span></span>

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<td class="diff-line-num new old_line" 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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>

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

</pre>

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

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num new old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff">     cmdclass={'install': compileInstall},</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"><span class="p">@@ -59,7 +35,7 @@</span> setup(</span>

</pre>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="diff">     author='Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson',</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff">     author_email='MSchubert@snm.ku.dk, jonsson.hakon@gmail.com',</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -55,7 +56,7 @@ Description: Use Debian packaged seqtk</td>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff">     license='LICENSE.txt',</span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/mapDamage</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/mapDamage</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">51,7 +151</span>,7 @@</span> def main():</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC59" class="line" lang="diff"><span class="p">@@ -1<span class="idiff left right">49,7 +149</span>,7 @@</span> def main():</span>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="diff">         sys.path.insert(0,path_to_mm)</span>

</pre>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff">     import mapdamage</span>

</pre>

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

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -66,12 +67,12 @@ Description: Use Debian packaged seqtk</td>

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

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff">                          "been intalled properly or current user does not\n"</span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/composition.py</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/composition.py</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="70" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">5,7 +35</span>,7 @@</span> def get_base_comp(filename,destination=F</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">3,7 +33</span>,7 @@</span> def get_base_comp(filename,destination=F</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="71" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff">     Gets the basecomposition of all the sequences in filename</span>

</pre>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="diff">     and returns the value to destination if given.</span>

</pre>

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

</pre>

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<td class="diff-line-num new_line old" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    path_to_seqtk = mapdamage.rscript.construct_path("seqtk",folder="seqtk")<span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    path_to_seqtk = "/usr/bin/seqtk"<span class="idiff left right"> </span></span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-    path_to_seqtk = mapdamage.rscript.construct_path("seqtk",folder="seqtk")</span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    path_to_seqtk = "/usr/bin/seqtk"</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff">     bases = {"A":0,"C":0,"G":0,"T":0}</span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff">     alp = ["A","C","G","T"]</span>

</pre>

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

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<td class="diff-line-num new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<br>

</li>

<li id="2d6120769b574994bf02fb43949cb89bc2e2c36c">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#2d6120769b574994bf02fb43949cb89bc2e2c36c"><strong>mapdamage/Rscripts/mapDamage.R</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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,20 +33,20 @@ draw.open.rect <- function(xleft, ybottom, xright, ytop, padding = 0) {</td>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="p">}</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">xpoints</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="n" style="color: #333;">xright</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xleft</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">padding</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xleft</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">padding</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xright</span><span class="p">)</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">    </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC36" class="line" lang="r"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">lines</span><span class="p">(</span><span class="n" style="color: #333;">xpoints</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="n" style="color: #333;">ytop</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ytop</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ybottom</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ybottom</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">col</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"darkgrey"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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

40

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

</pre>

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

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="r"><span class="n" style="color: #333;">plot.base.composition</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">tbl</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">base</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">color</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">around</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylabels.at</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xlabels</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">FALSE</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

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

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">xcoords</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">around</span><span class="o" style="font-weight: 600;">:</span><span class="m" style="color: #099;">-1</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">around</span><span class="p">)</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">  </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="r"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">plot.axis</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">yaxis.at</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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

45

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

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">axis</span><span class="p">(</span><span class="n" style="color: #333;">side</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">yaxis.at</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">labels</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">yaxis.at</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">==</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylabels.at</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">line</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">las</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cex.axis</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0.8</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">((</span><span class="n" style="color: #333;">yaxis.at</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">==</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">&&</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">yaxis.at</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">==</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylabels.at</span><span class="p">))</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="r"><span class="w" style="color: #bbb;">      </span><span class="n" style="color: #333;">mtext</span><span class="p">(</span><span class="s2" style="color: #d14;">"Frequency"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">side</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">line</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2.5</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cex</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0.6</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">  </span></span></span>

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">xlabels</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="r"><span class="w" style="color: #bbb;">      </span><span class="n" style="color: #333;">axis</span><span class="p">(</span><span class="n" style="color: #333;">side</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">labels</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xcoords</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">at</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xcoords</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">las</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cex.axis</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0.6</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,7 +64,7 @@ plot.base.composition <- function(tbl, base, color, around, ylabels.at = c(), xl</td>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">ycoords</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">NULL</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">for</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">in</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xcoords</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="r"><span class="w" style="color: #bbb;">      </span><span class="n" style="color: #333;">ycoords</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">ycoords</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">subtbl</span><span class="p">[(</span><span class="n" style="color: #333;">subtbl</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Pos</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">i</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">base</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">subtbl</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Total</span><span class="p">[(</span><span class="n" style="color: #333;">subtbl</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Pos</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">i</span><span class="p">)],</span><span class="n" style="color: #333;">na.rm</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">T</span><span class="p">))</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="r"><span class="w" style="color: #bbb;">      </span><span class="n" style="color: #333;">ycoords</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">append</span><span class="p">(</span><span class="n" style="color: #333;">ycoords</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mean</span><span class="p">(</span><span class="n" style="color: #333;">subtbl</span><span class="p">[(</span><span class="n" style="color: #333;">subtbl</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Pos</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">i</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">base</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">subtbl</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Total</span><span class="p">[(</span><span class="n" style="color: #333;">subtbl</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Pos</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">i</span><span class="p">)],</span><span class="n" style="color: #333;">na.rm</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">T</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">points</span><span class="p">(</span><span class="n" style="color: #333;">xcoords</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ycoords</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">pch</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">20</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">col</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">color</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">type</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"b"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="p">}</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -80,7 +80,7 @@ plot.base.composition <- function(tbl, base, color, around, ylabels.at = c(), xl</td>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">plot.frequencies</span><span class="p">(</span><span class="s2" style="color: #d14;">"3p"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">plot.axis</span><span class="p">(</span><span class="m" style="color: #099;">4</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">draw.open.rect</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">around</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0.5</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">  </span></span></span>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">par</span><span class="p">(</span><span class="n" style="color: #333;">mar</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2</span><span class="p">))</span></span>

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

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,8 +103,8 @@ calculate.mutation.table <- function(filename, length)</td>

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

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="r"><span class="n" style="color: #333;">write.mutation.table</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">tbl</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">columns</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"pos"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="s2" style="color: #d14;">"<span class="idiff left right">5p%s"</span></span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mismatch</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">tbl</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">is.na</span><span class="p">(</span><span class="n" style="color: #333;">tbl</span><span class="p">)]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0</span><span class="w" style="color: #bbb;"> </span><span class="c1" style="color: #998; font-style: italic;"># Python doesn't like NAs<span class="idiff left right">  </span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">columns</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"pos"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">sprintf</span><span class="p">(</span><span class="s2" style="color: #d14;">"<span class="idiff left">%s%s"</span></span><span class="p"><span class="idiff">,</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff right">end</span></span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mismatch</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">tbl</span><span class="p">[</span><span class="nf" style="color: #900; font-weight: 600;">is.na</span><span class="p">(</span><span class="n" style="color: #333;">tbl</span><span class="p">)]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0</span><span class="w" style="color: #bbb;"> </span><span class="c1" style="color: #998; font-style: italic;"># Python doesn't like NAs</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">write.table</span><span class="p">(</span><span class="n" style="color: #333;">tbl</span><span class="p">[</span><span class="n" style="color: #333;">tbl</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">End</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">==</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"Pos"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mismatch</span><span class="p">)],</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="r"><span class="w" style="color: #bbb;">                </span><span class="n" style="color: #333;">row.names</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">FALSE</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">col.names</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">columns</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="r"><span class="w" style="color: #bbb;">                </span><span class="n" style="color: #333;">sep</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"\t"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">quote</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">FALSE</span><span class="p">,</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -117,12 +117,12 @@ plot.mutations <- function(end, axis.at, start.i, end.i, modifier) {</td>

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<pre style="margin: 0;"> <span id="LC117" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">subtable</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">tbl</span><span class="p">[</span><span class="n" style="color: #333;">tbl</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">End</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">==</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"Pos"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mismatches</span><span class="p">)]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC118" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">rates</span><span class="w" style="color: #bbb;">    </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">rowSums</span><span class="p">(</span><span class="n" style="color: #333;">subtable</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">subtable</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Pos</span></span>

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

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<pre style="margin: 0;"> <span id="LC119" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">subtable</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">aggregate</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">Rate</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">rates</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">list</span><span class="p">(</span><span class="n" style="color: #333;">Pos</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">subtable</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Pos</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">sum</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">    </span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="120" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="r"></span>

</pre>

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121

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">lines</span><span class="p">(</span><span class="n" style="color: #333;">subtable</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Pos</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">*</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">modifier</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">subtable</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Rate</span><span class="p">,</span></span>

</pre>

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122

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122

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="r"><span class="w" style="color: #bbb;">          </span><span class="n" style="color: #333;">xlim</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">OPT.LENGTH</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylim</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">OPT.YMAX</span><span class="p">),</span></span>

</pre>

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123

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<td class="diff-line-num new_line" 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">

123

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="r"><span class="w" style="color: #bbb;">          </span><span class="n" style="color: #333;">col</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">color</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">lwd</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">width</span><span class="p">)</span></span>

</pre>

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124

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<td class="diff-line-num new_line" data-linenumber="124" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

124

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

125

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<td class="diff-line-num new_line old" data-linenumber="125" style="width: 35px; color: rgba(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="LC125" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">  </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

126

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="kc" style="font-weight: 600;">NA</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xlim</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="n" style="color: #333;">start.i</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">end.i</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylim</span><span class="o" style="font-weight: 600;">=</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">OPT.YMAX</span><span class="p">),</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">col</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"grey"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">lwd</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">type</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"l"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">xlab</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">""</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ylab</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">""</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">axes</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">FALSE</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

127

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">axis</span><span class="p">(</span><span class="n" style="color: #333;">side</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">labels</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">start.i</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">end.i</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">at</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">start.i</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">end.i</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">las</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cex.axis</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0.8</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">axis</span><span class="p">(</span><span class="n" style="color: #333;">side</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">axis.at</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">labels</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">TRUE</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">las</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cex.axis</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0.8</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -130,11 +130,11 @@ plot.mutations <- function(end, axis.at, start.i, end.i, modifier) {</td>

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<pre style="margin: 0;"> <span id="LC130" class="line" lang="r"><span class="w" style="color: #bbb;">      </span><span class="n" style="color: #333;">mtext</span><span class="p">(</span><span class="s2" style="color: #d14;">"Frequency"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">side</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">line</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">2.5</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cex</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0.6</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">draw.open.rect</span><span class="p">(</span><span class="n" style="color: #333;">start.i</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">OPT.YMAX</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">end.i</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">-0.01</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">padding</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0.5</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">  </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="r"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="k" style="font-weight: 600;">for</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">mismatch</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">in</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">MISMATCHES</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">do.plot</span><span class="p">(</span><span class="n" style="color: #333;">mut</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">modifier</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mismatch</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"grey"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="137" style="width: 35px; color: rgba(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="LC137" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">  </span></span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC137" class="line" lang="r"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">do.plot</span><span class="p">(</span><span class="n" style="color: #333;">mut</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">modifier</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">CLIPPING</span><span class="p">,</span><span class="w" style="color: #bbb;">   </span><span class="s2" style="color: #d14;">"orange"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">do.plot</span><span class="p">(</span><span class="n" style="color: #333;">mut</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">modifier</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">DELETIONS</span><span class="p">,</span><span class="w" style="color: #bbb;">  </span><span class="s2" style="color: #d14;">"green"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC140" class="line" lang="r"><span class="w" style="color: #bbb;">  </span><span class="n" style="color: #333;">do.plot</span><span class="p">(</span><span class="n" style="color: #333;">mut</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">end</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">modifier</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">INSERTIONS</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"purple"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="d97202d39b17c50fc83c976a09e5c652fcdb217c">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#d97202d39b17c50fc83c976a09e5c652fcdb217c"><strong>mapdamage/Rscripts/stats/function.R</strong></a>

<hr>

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1

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

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#Various useful functions</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="r"><span class="n" style="color: #333;">getPmat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">tmu</span><span class="p">,</span><span class="n" style="color: #333;">tv_ti_ratio</span><span class="p">,</span><span class="n" style="color: #333;">acgt</span><span class="p">){</span></span>

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

3

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

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Returns the evolutionary substitution matrix<span class="idiff left right">  </span></span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Returns the evolutionary substitution matrix</span></span>

</pre>

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4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">sum</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="o" style="font-weight: 600;">>=</span><span class="m" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="m" style="color: #099;">0</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">||</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">sum</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="o" style="font-weight: 600;"><=</span><span class="m" style="color: #099;">0</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="m" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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

5

</td>

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

5

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s2" style="color: #d14;">"The ACGT frequencies must be in the range 0 to 1"</span><span class="p">,</span><span class="n" style="color: #333;">stderr</span><span class="p">())</span></span>

</pre>

</td>

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

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

</td>

<td class="diff-line-num new_line 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">

</td>

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

<pre style="margin: 0;">-<span id="LC6" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">stop</span><span class="p">()</span><span class="w" style="color: #bbb;"><span class="idiff left right">       </span></span></span>

</pre>

</td>

</tr>

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

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

</td>

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

6

</td>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">stop</span><span class="p">()</span></span>

</pre>

</td>

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

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

7

</td>

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

7

</td>

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

<pre style="margin: 0;"> <span id="LC7" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

</pre>

</td>

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

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

8

</td>

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

8

</td>

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

<pre style="margin: 0;"> <span id="LC8" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">all.equal</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">sum</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">),</span><span class="m" style="color: #099;">1</span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="kc" style="font-weight: 600;">TRUE</span><span class="p">){</span></span>

</pre>

</td>

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

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

9

</td>

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

9

</td>

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

<pre style="margin: 0;"> <span id="LC9" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s2" style="color: #d14;">"The ACGT frequencies do not sum to 1"</span><span class="p">,</span><span class="n" style="color: #333;">stderr</span><span class="p">())</span></span>

</pre>

</td>

</tr>

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

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

10

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC10" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">stop</span><span class="p">()</span><span class="w" style="color: #bbb;"><span class="idiff left right">       </span></span></span>

</pre>

</td>

</tr>

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

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

</td>

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

10

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">stop</span><span class="p">()</span></span>

</pre>

</td>

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

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

11

</td>

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

11

</td>

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

<pre style="margin: 0;"> <span id="LC11" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

</pre>

</td>

</tr>

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

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

12

</td>

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

12

</td>

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

<pre style="margin: 0;"> <span id="LC12" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">tv_ti_ratio</span><span class="o" style="font-weight: 600;"><=</span><span class="m" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

</td>

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

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

13

</td>

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

13

</td>

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

<pre style="margin: 0;"> <span id="LC13" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s2" style="color: #d14;">"The transversion and transtition ratio cannot go under 0"</span><span class="p">,</span><span class="n" style="color: #333;">stderr</span><span class="p">())</span></span>

</pre>

</td>

</tr>

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

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

14

</td>

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

</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="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">stop</span><span class="p">()</span><span class="w" style="color: #bbb;"><span class="idiff left right">       </span></span></span>

</pre>

</td>

</tr>

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

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

</td>

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

14

</td>

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">stop</span><span class="p">()</span></span>

</pre>

</td>

</tr>

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

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

15

</td>

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

15

</td>

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

</pre>

</td>

</tr>

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

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

16

</td>

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

16

</td>

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Returns the substitution probability matrix.</span></span>

</pre>

</td>

</tr>

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

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

17

</td>

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

17

</td>

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

<pre style="margin: 0;"> <span id="LC17" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">identical</span><span class="p">(</span><span class="n" style="color: #333;">tv_ti_ratio</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">&&</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">identical</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">.25</span><span class="p">,</span><span class="m" style="color: #099;">.25</span><span class="p">,</span><span class="m" style="color: #099;">.25</span><span class="p">,</span><span class="m" style="color: #099;">.25</span><span class="p">))){</span></span>

</pre>

</td>

</tr>

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

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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">@@ -23,7 +23,7 @@ getPmat <- function(tmu,tv_ti_ratio,acgt){</td>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">E</span><span class="w" style="color: #bbb;">  </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">exp</span><span class="p">(</span><span class="n" style="color: #333;">r</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">values</span><span class="p">))</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#      Q        The eigen vector change of basis</span></span>

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

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#  M  ->   M<span class="idiff left right">   </span></span></span>

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

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<td class="diff-line-num new new_line" 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="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#  M  ->   M</span></span>

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

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#  ^       ^</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#  |B^-1   |B</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,8 +32,8 @@ getPmat <- function(tmu,tv_ti_ratio,acgt){</td>

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

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">out</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">solve</span><span class="p">(</span><span class="n" style="color: #333;">a</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">t</span><span class="p">(</span><span class="n" style="color: #333;">B</span><span class="p">),</span><span class="n" style="color: #333;">b</span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">E</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">%*%</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">t</span><span class="p">(</span><span class="n" style="color: #333;">B</span><span class="p">))</span><span class="c1" style="color: #998; font-style: italic;">#Little trick to avoid numerical difficulties</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">rownames</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"A"</span><span class="p">,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">,</span><span class="s2" style="color: #d14;">"G"</span><span class="p">,</span><span class="s2" style="color: #d14;">"T"</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">colnames</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"A"</span><span class="p">,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">,</span><span class="s2" style="color: #d14;">"G"</span><span class="p">,</span><span class="s2" style="color: #d14;">"T"</span><span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="nf" style="color: #900; font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">)</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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<td class="diff-line-num old old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line 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="LC36" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="nf" style="color: #900; font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" 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="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

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

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="r"><span class="n" style="color: #333;">jukesCantorPmat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">tmu</span><span class="p">){</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -49,22 +49,22 @@ qmatHKY85 <- function(tmu,tv_ti,acgt){</td>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#               |    pi_a*tv_ti    pi_c              pi_g * tv_ti   sum_4         |</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#returns this matrix</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#This could be replaced with the analytical formulas for the substitutions probabilities.</span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Qmat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">matrix</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">rep</span><span class="p">(</span><span class="n" style="color: #333;">acgt</span><span class="p">,</span><span class="m" style="color: #099;">4</span><span class="p">),</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">4</span><span class="p">,</span><span class="n" style="color: #333;">byrow</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">TRUE</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">Qmat</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Adjusting the transversions versus transitions</span></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#-  *  -  *<span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#*  -  *  -<span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#-  *  -  *<span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#*  -  *  -<span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#-  *  -  *</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#*  -  *  -</span></span>

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<td class="diff-line-num new new_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

59

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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="LC59" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#-  *  -  *</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

60

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

<pre style="margin: 0;">+<span id="LC60" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#*  -  *  -</span></span>

</pre>

</td>

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

61

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

61

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

<pre style="margin: 0;"> <span id="LC61" class="line" lang="r"></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

</td>

<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

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

<pre style="margin: 0;"> <span id="LC62" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="m" style="color: #099;">2</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">tv_ti</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="m" style="color: #099;">2</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="m" style="color: #099;">4</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">tv_ti</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="m" style="color: #099;">4</span><span class="p">]</span></span>

</pre>

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

64

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

64

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

<pre style="margin: 0;"> <span id="LC64" class="line" lang="r"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

65

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">tv_ti</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">]</span></span>

</pre>

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

66

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

66

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="m" style="color: #099;">3</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">tv_ti</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="m" style="color: #099;">3</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

67

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<td class="diff-line-num new_line old" data-linenumber="67" style="width: 35px; color: rgba(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="LC67" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">    </span></span></span>

</pre>

</td>

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

</td>

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

67

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

<pre style="margin: 0;">+<span id="LC67" class="line" lang="r"></span>

</pre>

</td>

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

68

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

68

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">3</span><span class="p">,</span><span class="m" style="color: #099;">2</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">tv_ti</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">3</span><span class="p">,</span><span class="m" style="color: #099;">2</span><span class="p">]</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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<td class="diff-line-num new_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

69

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">3</span><span class="p">,</span><span class="m" style="color: #099;">4</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">tv_ti</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">Qmat</span><span class="p">[</span><span class="m" style="color: #099;">3</span><span class="p">,</span><span class="m" style="color: #099;">4</span><span class="p">]</span></span>

</pre>

</td>

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

70

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

70

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

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

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -73,12 +73,12 @@ qmatHKY85 <- function(tmu,tv_ti,acgt){</td>

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<td class="diff-line-num old_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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<td class="diff-line-num new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

73

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

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

</pre>

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

74

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

74

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">diag</span><span class="p">(</span><span class="n" style="color: #333;">Qmat</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">Qmat</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">sum</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

75

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

75

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

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

</pre>

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76

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<td class="diff-line-num new_line old" data-linenumber="76" style="width: 35px; color: rgba(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="LC76" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Qmat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">tmu</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">*</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">Qmat</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Qmat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">tmu</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">*</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">Qmat</span></span>

</pre>

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

77

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="nf" style="color: #900; font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">Qmat</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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

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

</pre>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="r"><span class="n" style="color: #333;">metroDesc</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">lpr</span><span class="p">,</span><span class="n" style="color: #333;">lol</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="81" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="81" style="width: 35px; color: rgba(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="LC81" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;"># the logic in the Metropolis-Hastings step<span class="idiff left right"> </span></span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;"># the logic in the Metropolis-Hastings step</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">stopifnot</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nf" style="color: #900; font-weight: 600;">is.na</span><span class="p">(</span><span class="n" style="color: #333;">lpr</span><span class="p">))</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">stopifnot</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="nf" style="color: #900; font-weight: 600;">is.na</span><span class="p">(</span><span class="n" style="color: #333;">lol</span><span class="p">))</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">log</span><span class="p">(</span><span class="n" style="color: #333;">runif</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">))</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">lpr</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">lol</span><span class="p">){</span></span>

</pre>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -89,7 +89,7 @@ metroDesc <- function(lpr,lol){</td>

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

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

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="r"></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="r"><span class="n" style="color: #333;">genOverHang</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">la</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="92" style="width: 35px; color: rgba(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="LC92" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Currently not used in the main code but could used to generate<span class="idiff left right"> </span></span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Currently not used in the main code but could used to generate</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#overhangs like Philip</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">r</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">runif</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">i</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">-1</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -143,7 +143,7 @@ seqProbVecLambda <- function(lambda,lambda_disp,m,fo_only=NA,re_only=NA){</td>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC144" class="line" lang="r"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC145" class="line" lang="r"></span>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#The following is an MC simulation code to mimic the<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#The following is an MC simulation code to mimic the</span></span>

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<pre style="margin: 0;"> <span id="LC147" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#nick frequency part in the model from Philip</span></span>

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<pre style="margin: 0;"> <span id="LC148" class="line" lang="r"><span class="n" style="color: #333;">seqProbVecNuWithLengths</span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cxxfunction</span><span class="p">(</span><span class="n" style="color: #333;">methods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">signature</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC149" class="line" lang="r"><span class="w" style="color: #bbb;">                                      </span><span class="n" style="color: #333;">I_la</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"numeric"</span><span class="p">,</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -162,7 +162,7 @@ seqProbVecNuWithLengths<- cxxfunction(methods::signature(</td>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="r"><span class="s1" style="color: #d14;">                      double r = ((double) rand() / (RAND_MAX));</span></span>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="r"><span class="s1" style="color: #d14;">                      int i = -1;</span></span>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="r"><span class="s1" style="color: #d14;">                      double p = 0;</span></span>

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="r"><span class="s1" style="color: #d14;">                      double term = -500;<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC165" class="line" lang="r"><span class="s1" style="color: #d14;">                      double term = -500;</span></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="r"><span class="s1" style="color: #d14;">                      while (p<r){</span></span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="r"><span class="s1" style="color: #d14;">                          if (i==-1){</span></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="r"><span class="s1" style="color: #d14;">                              term = 1;</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -175,7 +175,7 @@ seqProbVecNuWithLengths<- cxxfunction(methods::signature(</td>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="r"><span class="s1" style="color: #d14;">                      return(i);</span></span>

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="r"><span class="s1" style="color: #d14;">                  }</span></span>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="r"><span class="s1" style="color: #d14;">                  '</span><span class="p">,</span><span class="n" style="color: #333;">body</span><span class="o" style="font-weight: 600;">=</span><span class="w" style="color: #bbb;"> </span><span class="s1" style="color: #d14;">'</span></span>

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<td class="diff-line-num old old_line" data-linenumber="178" style="width: 35px; color: rgba(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="LC178" class="line" lang="r"><span class="s1" style="color: #d14;">              srand(time(0));<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="r"><span class="s1" style="color: #d14;">              srand(time(0));</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="r"><span class="s1" style="color: #d14;">        Rcpp::NumericVector la(I_la);</span></span>

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<td class="diff-line-num old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="r"><span class="s1" style="color: #d14;">        Rcpp::NumericVector la_disp(I_la_disp);</span></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="r"><span class="s1" style="color: #d14;">        Rcpp::NumericVector nu(I_nu);</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -199,7 +199,7 @@ seqProbVecNuWithLengths<- cxxfunction(methods::signature(</td>

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<td class="diff-line-num old_line" 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">

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="r"><span class="s1" style="color: #d14;">                double left_o_hang = genOverHang(la[0],la_disp[0]);</span></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="r"><span class="s1" style="color: #d14;">                double right_o_hang = genOverHang(la[0],la_disp[0]);</span></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="r"><span class="s1" style="color: #d14;">                double o_hang  = left_o_hang+right_o_hang;</span></span>

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<pre style="margin: 0;">-<span id="LC202" class="line" lang="r"><span class="s1" style="color: #d14;">//<span class="idiff left right">              </span></span></span>

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<pre style="margin: 0;">+<span id="LC202" class="line" lang="r"><span class="s1" style="color: #d14;">//</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="r"><span class="s1" style="color: #d14;">                if (o_hang>=les(i)){</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="r"><span class="s1" style="color: #d14;">                    //Single stranded sequence</span></span>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="r"><span class="s1" style="color: #d14;">                    for (int j = 0; j <les(i);j++){</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); 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="211" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -211,8 +211,8 @@ seqProbVecNuWithLengths<- cxxfunction(methods::signature(</td>

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<td class="diff-line-num old_line" data-linenumber="211" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC211" class="line" lang="r"><span class="s1" style="color: #d14;">                        for (int j = 0; j <(les[i]-right_o_hang);j++){</span></span>

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<pre style="margin: 0;"> <span id="LC212" class="line" lang="r"><span class="s1" style="color: #d14;">                            output(j) = output(j)+1;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="r"><span class="s1" style="color: #d14;">                        }</span></span>

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<pre style="margin: 0;">-<span id="LC214" class="line" lang="r"><span class="s1" style="color: #d14;">                        //The right overhang is always G>A for the double stranded but<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC215" class="line" lang="r"><span class="s1" style="color: #d14;">                        //Here we will make the assumption that the pattern is symmetric<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC214" class="line" lang="r"><span class="s1" style="color: #d14;">                        //The right overhang is always G>A for the double stranded but</span></span>

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<pre style="margin: 0;">+<span id="LC215" class="line" lang="r"><span class="s1" style="color: #d14;">                        //Here we will make the assumption that the pattern is symmetric</span></span>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="r"><span class="s1" style="color: #d14;">                        //for practical reasons We can\'t  do that ....</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="r"><span class="s1" style="color: #d14;">                    }else {</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="r"><span class="s1" style="color: #d14;">                        Rcpp::NumericVector sa = floor(runif(1,0,les[i]-o_hang))+left_o_hang;</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -258,7 +258,7 @@ pDam <- function(th,ded,des,la,nu,lin){</td>

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

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<pre style="margin: 0;"> <span id="LC259" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC260" class="line" lang="r"><span class="n" style="color: #333;">logLikFunOneBaseSlow</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">Gen</span><span class="p">,</span><span class="n" style="color: #333;">S</span><span class="p">,</span><span class="n" style="color: #333;">Theta</span><span class="p">,</span><span class="n" style="color: #333;">deltad</span><span class="p">,</span><span class="n" style="color: #333;">deltas</span><span class="p">,</span><span class="n" style="color: #333;">laVec</span><span class="p">,</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="n" style="color: #333;">lin</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC261" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Calculates the log likelihood using R, a C++ version is available<span class="idiff left right">  </span></span></span>

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<pre style="margin: 0;">+<span id="LC261" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Calculates the log likelihood using R, a C++ version is available</span></span>

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<pre style="margin: 0;"> <span id="LC262" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">ll</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC263" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">for</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">in</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="nf" style="color: #900; font-weight: 600;">length</span><span class="p">(</span><span class="n" style="color: #333;">laVec</span><span class="p">)){</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#Get the damage probabilities</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -268,7 +268,7 @@ logLikFunOneBaseSlow <- function(Gen,S,Theta,deltad,deltas,laVec,nuVec,m,lin){</td>

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="nf" style="color: #900; font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">ll</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="r"><span class="p">}</span></span>

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

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<td class="diff-line-num old old_line" data-linenumber="271" style="width: 35px; color: rgba(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="LC271" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#The same logic as in logLikFunOneBaseSlow except using a compiled code<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC271" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#The same logic as in logLikFunOneBaseSlow except using a compiled code</span></span>

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#to do the hard work</span></span>

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="r"><span class="n" style="color: #333;">logLikFunOneBaseFast</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cxxfunction</span><span class="p">(</span><span class="n" style="color: #333;">methods</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">signature</span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="r"><span class="w" style="color: #bbb;">                                      </span><span class="n" style="color: #333;">I_Gen</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"numeric"</span><span class="p">,</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -333,7 +333,7 @@ return(ret);</td>

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<pre style="margin: 0;"> <span id="LC333" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC334" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC335" class="line" lang="r"><span class="n" style="color: #333;">logLikAll</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">,</span><span class="n" style="color: #333;">Theta</span><span class="p">,</span><span class="n" style="color: #333;">deltad</span><span class="p">,</span><span class="n" style="color: #333;">deltas</span><span class="p">,</span><span class="n" style="color: #333;">laVec</span><span class="p">,</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">){</span></span>

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<pre style="margin: 0;">-<span id="LC336" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Calculates the logLikelihood for all the bases by calling<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC336" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Calculates the logLikelihood for all the bases by calling</span></span>

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<pre style="margin: 0;"> <span id="LC337" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;"># logLikFunOneBaseFast for each base</span></span>

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<pre style="margin: 0;"> <span id="LC338" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">deltad</span><span class="o" style="font-weight: 600;"><</span><span class="m" style="color: #099;">0</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">||</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">deltad</span><span class="o" style="font-weight: 600;">></span><span class="m" style="color: #099;">1</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">||</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">deltas</span><span class="o" style="font-weight: 600;"><</span><span class="m" style="color: #099;">0</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">||</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">deltas</span><span class="o" style="font-weight: 600;">></span><span class="m" style="color: #099;">1</span><span class="w" style="color: #bbb;">  </span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC339" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="nf" style="color: #900; font-weight: 600;">return</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="kc" style="font-weight: 600;">Inf</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="341" style="width: 35px; color: rgba(0,0,0,0.3); 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="341" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -341,8 +341,8 @@ logLikAll <- function(dat,Theta,deltad,deltas,laVec,nuVec,m){</td>

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<pre style="margin: 0;"> <span id="LC341" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#A,C,G and T</span></span>

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<pre style="margin: 0;"> <span id="LC342" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC343" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">deb</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">0</span></span>

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<pre style="margin: 0;">-<span id="LC344" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">-<span id="LC345" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Asub</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.C"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.G"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.T"</span><span class="p">]</span><span class="w" style="color: #bbb;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC344" class="line" lang="r"></span>

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<pre style="margin: 0;">+<span id="LC345" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Asub</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.C"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.G"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.T"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC346" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">ALL</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">logLikFunOneBaseFast</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A"</span><span class="p">],</span><span class="n" style="color: #333;">cbind</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A"</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Asub</span><span class="p">,</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.C"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.G"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.T"</span><span class="p">]),</span><span class="n" style="color: #333;">Theta</span><span class="p">,</span><span class="n" style="color: #333;">deltad</span><span class="p">,</span><span class="n" style="color: #333;">deltas</span><span class="p">,</span><span class="n" style="color: #333;">laVec</span><span class="p">,</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC347" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">deb</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC348" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">ALLSlow</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">logLikFunOneBaseSlow</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A"</span><span class="p">],</span><span class="n" style="color: #333;">cbind</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A"</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Asub</span><span class="p">,</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.C"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.G"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"A.T"</span><span class="p">]),</span><span class="n" style="color: #333;">Theta</span><span class="p">,</span><span class="n" style="color: #333;">deltad</span><span class="p">,</span><span class="n" style="color: #333;">deltas</span><span class="p">,</span><span class="n" style="color: #333;">laVec</span><span class="p">,</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="355" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -355,7 +355,7 @@ logLikAll <- function(dat,Theta,deltad,deltas,laVec,nuVec,m){</td>

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<pre style="margin: 0;"> <span id="LC355" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">CLLSlow</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">logLikFunOneBaseSlow</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">],</span><span class="n" style="color: #333;">cbind</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"C.A"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Csub</span><span class="p">,</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"C.G"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"C.T"</span><span class="p">]),</span><span class="n" style="color: #333;">Theta</span><span class="p">,</span><span class="n" style="color: #333;">deltad</span><span class="p">,</span><span class="n" style="color: #333;">deltas</span><span class="p">,</span><span class="n" style="color: #333;">laVec</span><span class="p">,</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="m" style="color: #099;">2</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC356" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">stopifnot</span><span class="p">(</span><span class="n" style="color: #333;">all.equal</span><span class="p">(</span><span class="n" style="color: #333;">CLL</span><span class="p">,</span><span class="n" style="color: #333;">CLLSlow</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC357" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC358" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">    </span></span></span>

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

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<pre style="margin: 0;"> <span id="LC359" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC360" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Gsub</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.A"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.C"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.T"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC361" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">GLL</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">logLikFunOneBaseFast</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G"</span><span class="p">],</span><span class="n" style="color: #333;">cbind</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.A"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.C"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G"</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Gsub</span><span class="p">,</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.T"</span><span class="p">]),</span><span class="n" style="color: #333;">Theta</span><span class="p">,</span><span class="n" style="color: #333;">deltad</span><span class="p">,</span><span class="n" style="color: #333;">deltas</span><span class="p">,</span><span class="n" style="color: #333;">laVec</span><span class="p">,</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="m" style="color: #099;">3</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="363" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -363,7 +363,7 @@ logLikAll <- function(dat,Theta,deltad,deltas,laVec,nuVec,m){</td>

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<pre style="margin: 0;"> <span id="LC363" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">GLLSlow</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">logLikFunOneBaseSlow</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G"</span><span class="p">],</span><span class="n" style="color: #333;">cbind</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.A"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.C"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G"</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Gsub</span><span class="p">,</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.T"</span><span class="p">]),</span><span class="n" style="color: #333;">Theta</span><span class="p">,</span><span class="n" style="color: #333;">deltad</span><span class="p">,</span><span class="n" style="color: #333;">deltas</span><span class="p">,</span><span class="n" style="color: #333;">laVec</span><span class="p">,</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="m" style="color: #099;">3</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC364" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">stopifnot</span><span class="p">(</span><span class="n" style="color: #333;">all.equal</span><span class="p">(</span><span class="n" style="color: #333;">CLL</span><span class="p">,</span><span class="n" style="color: #333;">CLLSlow</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC365" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC366" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC366" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC367" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">Tsub</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"T.A"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"T.C"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"T.G"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC368" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">TLL</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">logLikFunOneBaseFast</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"T"</span><span class="p">],</span><span class="n" style="color: #333;">cbind</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"T.A"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"T.C"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"T.G"</span><span class="p">],</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"T"</span><span class="p">]</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">Tsub</span><span class="p">),</span><span class="n" style="color: #333;">Theta</span><span class="p">,</span><span class="n" style="color: #333;">deltad</span><span class="p">,</span><span class="n" style="color: #333;">deltas</span><span class="p">,</span><span class="n" style="color: #333;">laVec</span><span class="p">,</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">m</span><span class="p">,</span><span class="m" style="color: #099;">4</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC369" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">deb</span><span class="p">){</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="375" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -375,7 +375,7 @@ logLikAll <- function(dat,Theta,deltad,deltas,laVec,nuVec,m){</td>

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<pre style="margin: 0;"> <span id="LC375" class="line" lang="r"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC376" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC377" class="line" lang="r"><span class="n" style="color: #333;">getParams</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">cp</span><span class="p">){</span></span>

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378

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<td class="diff-line-num new_line old" data-linenumber="378" style="width: 35px; color: rgba(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="LC378" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Utility function nice to update the MCMC iterations matrix<span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC378" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Utility function nice to update the MCMC iterations matrix</span></span>

</pre>

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379

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<pre style="margin: 0;"> <span id="LC379" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="nf" style="color: #900; font-weight: 600;">return</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="n" style="color: #333;">cp</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Theta</span><span class="p">,</span><span class="n" style="color: #333;">cp</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Rho</span><span class="p">,</span><span class="n" style="color: #333;">cp</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">DeltaD</span><span class="p">,</span><span class="n" style="color: #333;">cp</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">DeltaS</span><span class="p">,</span><span class="n" style="color: #333;">cp</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Lambda</span><span class="p">,</span><span class="n" style="color: #333;">cp</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">LambdaRight</span><span class="p">,</span><span class="n" style="color: #333;">cp</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">LambdaDisp</span><span class="p">,</span><span class="n" style="color: #333;">cp</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">Nu</span><span class="p">))</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC380" class="line" lang="r"><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="381" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC381" class="line" lang="r"></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -385,7 +385,7 @@ plotTrace<- function(dat,main,k=111){</td>

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

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<pre style="margin: 0;"> <span id="LC385" class="line" lang="r"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC386" class="line" lang="r"></span>

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<td class="diff-line-num old_line" data-linenumber="387" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC387" class="line" lang="r"><span class="n" style="color: #333;">plotEverything</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">mcmcOut</span><span class="p">,</span><span class="n" style="color: #333;">hi</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">pl</span><span class="p">,</span><span class="n" style="color: #333;">thin</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">100</span><span class="p">){</span></span>

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<td class="diff-line-num new_line old" data-linenumber="388" style="width: 35px; color: rgba(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="LC388" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Plots the MCMC traceplot in the form of a running median and<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="388" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC388" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Plots the MCMC traceplot in the form of a running median and</span></span>

</pre>

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389

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<td class="diff-line-num new_line" data-linenumber="389" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC389" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#histogram of the MCMC iterations</span></span>

</pre>

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390

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<td class="diff-line-num new_line" data-linenumber="390" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

390

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<pre style="margin: 0;"> <span id="LC390" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">sum</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">same_overhangs</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">FALSE</span><span class="p">,</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC391" class="line" lang="r"><span class="w" style="color: #bbb;">                    </span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">fix_disp</span><span class="o" style="font-weight: 600;">==</span><span class="kc" style="font-weight: 600;">FALSE</span><span class="p">,</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="438" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -438,7 +438,7 @@ plotEverything <- function(mcmcOut,hi=0,pl,thin=100){</td>

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438

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438

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<pre style="margin: 0;"> <span id="LC438" class="line" lang="r"><span class="p">}</span></span>

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439

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439

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

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440

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<pre style="margin: 0;"> <span id="LC440" class="line" lang="r"><span class="n" style="color: #333;">accRat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">){</span></span>

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441

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<pre style="margin: 0;">-<span id="LC441" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#A rough measure of the acceptance ratio<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC441" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#A rough measure of the acceptance ratio</span></span>

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442

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<pre style="margin: 0;"> <span id="LC442" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="nf" style="color: #900; font-weight: 600;">return</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">length</span><span class="p">(</span><span class="n" style="color: #333;">unique</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">))</span><span class="o" style="font-weight: 600;">/</span><span class="nf" style="color: #900; font-weight: 600;">length</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">))</span></span>

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443

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<pre style="margin: 0;"> <span id="LC443" class="line" lang="r"><span class="p">}</span></span>

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444

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="467" style="width: 35px; color: rgba(0,0,0,0.3); 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="467" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -467,7 +467,7 @@ adjustPropVar <- function(mcmc,propVar){</td>

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467

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="r"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC468" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="r"><span class="n" style="color: #333;">runGibbs</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="p">,</span><span class="n" style="color: #333;">iter</span><span class="p">){</span></span>

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470

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<pre style="margin: 0;">-<span id="LC470" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Sampling over the conditional posterior distribution<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC470" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Sampling over the conditional posterior distribution</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#for the parameters.</span></span>

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<pre style="margin: 0;"> <span id="LC472" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">esti</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">matrix</span><span class="p">(</span><span class="n" style="color: #333;">nrow</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">iter</span><span class="p">,</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">9</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">colnames</span><span class="p">(</span><span class="n" style="color: #333;">esti</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"Theta"</span><span class="p">,</span><span class="s2" style="color: #d14;">"Rho"</span><span class="p">,</span><span class="s2" style="color: #d14;">"DeltaD"</span><span class="p">,</span><span class="s2" style="color: #d14;">"DeltaS"</span><span class="p">,</span><span class="s2" style="color: #d14;">"Lambda"</span><span class="p">,</span><span class="s2" style="color: #d14;">"LambdaRight"</span><span class="p">,</span><span class="s2" style="color: #d14;">"LambdaDisp"</span><span class="p">,</span><span class="s2" style="color: #d14;">"Nu"</span><span class="p">,</span><span class="s2" style="color: #d14;">"LogLik"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -492,7 +492,7 @@ runGibbs <- function(cu_pa,iter){</td>

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<td class="diff-line-num old_line" data-linenumber="492" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="r"><span class="w" style="color: #bbb;">            </span><span class="c1" style="color: #998; font-style: italic;">#Update the nu parameter by via MC estimation</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="493" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="r"><span class="w" style="color: #bbb;">            </span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;"><-</span><span class="n" style="color: #333;">updateNu</span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="494" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="p">}</span></span>

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<td class="diff-line-num old old_line" data-linenumber="495" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="495" style="width: 35px; color: rgba(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="LC495" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">esti</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="m" style="color: #099;">8</span><span class="p">)]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">getParams</span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="p">)</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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495

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<pre style="margin: 0;">+<span id="LC495" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">esti</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="m" style="color: #099;">8</span><span class="p">)]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">getParams</span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="496" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">esti</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="s2" style="color: #d14;">"LogLik"</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">logLikAll</span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">dat</span><span class="p">,</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">ThetaMat</span><span class="p">,</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">DeltaD</span><span class="p">,</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">DeltaS</span><span class="p">,</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">laVec</span><span class="p">,</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">m</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="497" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC497" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">%%</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1000</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">&&</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">verbose</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="498" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC498" class="line" lang="r"><span class="w" style="color: #bbb;">            </span><span class="n" style="color: #333;">cat</span><span class="p">(</span><span class="s2" style="color: #d14;">"MCMC-Iter\t"</span><span class="p">,</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="s2" style="color: #d14;">"\t"</span><span class="p">,</span><span class="n" style="color: #333;">esti</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="s2" style="color: #d14;">"LogLik"</span><span class="p">],</span><span class="s2" style="color: #d14;">"\n"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); 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="504" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -504,7 +504,7 @@ runGibbs <- function(cu_pa,iter){</td>

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<td class="diff-line-num old_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="504" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC504" class="line" lang="r"></span>

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<td class="diff-line-num old_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="505" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC505" class="line" lang="r"><span class="n" style="color: #333;">simPredCheck</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">,</span><span class="n" style="color: #333;">output</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

506

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<td class="diff-line-num new_line" data-linenumber="506" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC506" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Simulates one draw from the posterior predictive distribution</span></span>

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<td class="diff-line-num old old_line" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

507

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<td class="diff-line-num new_line old" data-linenumber="507" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC507" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#and the probability of a C>T substitution because of a cytosine<span class="idiff left right"> </span></span></span>

</pre>

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507

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<pre style="margin: 0;">+<span id="LC507" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#and the probability of a C>T substitution because of a cytosine</span></span>

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508

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<pre style="margin: 0;"> <span id="LC508" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#demnation.</span></span>

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509

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509

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<pre style="margin: 0;"> <span id="LC509" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">bases</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">da</span><span class="p">[,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"A"</span><span class="p">,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">,</span><span class="s2" style="color: #d14;">"G"</span><span class="p">,</span><span class="s2" style="color: #d14;">"T"</span><span class="p">)]</span></span>

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510

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<td class="diff-line-num new_line" data-linenumber="510" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

510

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<pre style="margin: 0;"> <span id="LC510" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Constructing the lambda vector</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="541" style="width: 35px; color: rgba(0,0,0,0.3); 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="541" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -541,12 +541,12 @@ simPredCheck <- function(da,output){</td>

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<pre style="margin: 0;"> <span id="LC541" class="line" lang="r"><span class="w" style="color: #bbb;">                                         </span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">mLe</span><span class="p">,</span></span>

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542

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542

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<pre style="margin: 0;"> <span id="LC542" class="line" lang="r"><span class="w" style="color: #bbb;">                                         </span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">forward_only</span><span class="p">,</span></span>

</pre>

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543

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543

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<pre style="margin: 0;"> <span id="LC543" class="line" lang="r"><span class="w" style="color: #bbb;">                                         </span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">nuSamples</span><span class="p">,</span></span>

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544

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<pre style="margin: 0;">-<span id="LC544" class="line" lang="r"><span class="w" style="color: #bbb;">                                         </span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">ds_protocol</span><span class="p">)</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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544

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<pre style="margin: 0;">+<span id="LC544" class="line" lang="r"><span class="w" style="color: #bbb;">                                         </span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">ds_protocol</span><span class="p">)</span></span>

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545

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<pre style="margin: 0;"> <span id="LC545" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">nuVec</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="n" style="color: #333;">nuVec</span><span class="p">,</span><span class="n" style="color: #333;">rev</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nuVec</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC546" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC547" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">nuVec</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">nuVec</span></span>

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<pre style="margin: 0;"> <span id="LC548" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

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<pre style="margin: 0;">-<span id="LC549" class="line" lang="r"><span class="w" style="color: #bbb;"><span class="idiff left right">    </span></span></span>

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<pre style="margin: 0;">+<span id="LC549" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC550" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Sample the other parameters</span></span>

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<pre style="margin: 0;"> <span id="LC551" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">des</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">out</span><span class="p">[,</span><span class="s2" style="color: #d14;">"DeltaS"</span><span class="p">],</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC552" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">ded</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">sample</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">out</span><span class="p">[,</span><span class="s2" style="color: #d14;">"DeltaD"</span><span class="p">],</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -562,10 +562,10 @@ simPredCheck <- function(da,output){</td>

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<pre style="margin: 0;"> <span id="LC562" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">subs</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">matrix</span><span class="p">(</span><span class="kc" style="font-weight: 600;">NA</span><span class="p">,</span><span class="n" style="color: #333;">nrow</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">dat</span><span class="p">),</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">4</span><span class="o" style="font-weight: 600;">+</span><span class="nf" style="color: #900; font-weight: 600;">length</span><span class="p">(</span><span class="n" style="color: #333;">coln</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC563" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">colnames</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"A"</span><span class="p">,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">,</span><span class="s2" style="color: #d14;">"G"</span><span class="p">,</span><span class="s2" style="color: #d14;">"T"</span><span class="p">,</span><span class="n" style="color: #333;">coln</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC564" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;">-<span id="LC565" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">damProb</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">rep</span><span class="p">(</span><span class="kc" style="font-weight: 600;">NA</span><span class="p">,</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">dat</span><span class="p">))</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC566" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">damProbGA</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">damProb</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC565" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">damProb</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">rep</span><span class="p">(</span><span class="kc" style="font-weight: 600;">NA</span><span class="p">,</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">dat</span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC566" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">damProbGA</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">damProb</span></span>

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<pre style="margin: 0;"> <span id="LC567" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">for</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">i</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">in</span><span class="w" style="color: #bbb;"> </span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">dat</span><span class="p">)){</span></span>

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<td class="diff-line-num new_line old" data-linenumber="568" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC568" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#Construct the site specific probabilities<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC568" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#Construct the site specific probabilities</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC569" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">pct</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">nuVec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">laVec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">des</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ded</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">laVec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC570" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">pga</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">nuVec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">])</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="n" style="color: #333;">laVec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">des</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ded</span><span class="o" style="font-weight: 600;">*</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">laVec</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]))</span></span>

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571

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

571

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<pre style="margin: 0;"> <span id="LC571" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">pDamMat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">matrix</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); 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="574" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -574,11 +574,11 @@ simPredCheck <- function(da,output){</td>

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574

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<td class="diff-line-num new_line" data-linenumber="574" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC574" class="line" lang="r"><span class="w" style="color: #bbb;">                         </span><span class="n" style="color: #333;">pga</span><span class="p">,</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">pga</span><span class="p">,</span><span class="m" style="color: #099;">0</span><span class="p">,</span></span>

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575

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575

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<pre style="margin: 0;"> <span id="LC575" class="line" lang="r"><span class="w" style="color: #bbb;">                         </span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="m" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC576" class="line" lang="r"><span class="w" style="color: #bbb;">                         </span><span class="p">),</span><span class="n" style="color: #333;">nrow</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">4</span><span class="p">,</span><span class="n" style="color: #333;">byrow</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">TRUE</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="577" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC577" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">ThetapDam</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">pDamMat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">%*%</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">pmat</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC577" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">ThetapDam</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">pDamMat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">%*%</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">pmat</span></span>

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578

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578

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<pre style="margin: 0;"> <span id="LC578" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#Calculate the probability C.T due to cytosine demanation</span></span>

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579

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<td class="diff-line-num new_line old" data-linenumber="579" style="width: 35px; color: rgba(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="LC579" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">damProb</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ptransCC</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pct</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">ptransCC</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pct</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ptransCT</span><span class="p">)</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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580

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<td class="diff-line-num new_line old" data-linenumber="579" style="width: 35px; color: rgba(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="LC580" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#Do not forget the reverse complement<span class="idiff left right"> </span></span></span>

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581

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<td class="diff-line-num new_line old" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC581" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">damProbGA</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ptransGG</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pga</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">ptransGG</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pga</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ptransGA</span><span class="p">)</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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579

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<pre style="margin: 0;">+<span id="LC579" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">damProb</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ptransCC</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pct</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">ptransCC</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pct</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ptransCT</span><span class="p">)</span></span>

</pre>

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580

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<pre style="margin: 0;">+<span id="LC580" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#Do not forget the reverse complement</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC581" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">damProbGA</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ptransGG</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pga</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">ptransGG</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">pga</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">ptransGA</span><span class="p">)</span></span>

</pre>

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582

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

582

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<pre style="margin: 0;"> <span id="LC582" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#Then draw from a multinomial distribution</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="583" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

583

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583

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<pre style="margin: 0;"> <span id="LC583" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"A.C"</span><span class="p">,</span><span class="s2" style="color: #d14;">"A.G"</span><span class="p">,</span><span class="s2" style="color: #d14;">"A.T"</span><span class="p">)]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">t</span><span class="p">(</span><span class="n" style="color: #333;">rmultinom</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">dat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="s2" style="color: #d14;">"A"</span><span class="p">],</span><span class="n" style="color: #333;">ThetapDam</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="p">,]))[</span><span class="m" style="color: #099;">-1</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">dat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="s2" style="color: #d14;">"A"</span><span class="p">]</span></span>

</pre>

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584

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

584

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<pre style="margin: 0;"> <span id="LC584" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"C.A"</span><span class="p">,</span><span class="s2" style="color: #d14;">"C.G"</span><span class="p">,</span><span class="s2" style="color: #d14;">"C.T"</span><span class="p">)]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">t</span><span class="p">(</span><span class="n" style="color: #333;">rmultinom</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">dat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">],</span><span class="n" style="color: #333;">ThetapDam</span><span class="p">[</span><span class="m" style="color: #099;">2</span><span class="p">,]))[</span><span class="m" style="color: #099;">-2</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">dat</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="602" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -602,7 +602,7 @@ calcSampleStats <- function(da,X){</td>

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<pre style="margin: 0;"> <span id="LC602" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC603" class="line" lang="r"><span class="n" style="color: #333;">postPredCheck</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">function</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">,</span><span class="n" style="color: #333;">output</span><span class="p">,</span><span class="n" style="color: #333;">samples</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">10000</span><span class="p">){</span></span>

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<td class="diff-line-num new_line" data-linenumber="604" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC604" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Plots the 95% posterior predictive intervals with the data as lines.</span></span>

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<td class="diff-line-num old old_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC605" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Returns the site specific probability of a C>T or G>A substitution<span class="idiff left right"> </span></span></span>

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<td class="diff-line-num new new_line" data-linenumber="605" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC605" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Returns the site specific probability of a C>T or G>A substitution</span></span>

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<td class="diff-line-num new_line" data-linenumber="606" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC606" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#because of a cytosine demnation.</span></span>

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<pre style="margin: 0;"> <span id="LC607" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">CTs</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">matrix</span><span class="p">(</span><span class="kc" style="font-weight: 600;">NA</span><span class="p">,</span><span class="n" style="color: #333;">nrow</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">),</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="608" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC608" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">GAs</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">matrix</span><span class="p">(</span><span class="kc" style="font-weight: 600;">NA</span><span class="p">,</span><span class="n" style="color: #333;">nrow</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">),</span><span class="n" style="color: #333;">ncol</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="635" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -635,28 +635,28 @@ postPredCheck <- function(da,output,samples=10000){</td>

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635

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<pre style="margin: 0;"> <span id="LC635" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

636

</td>

<td class="diff-line-num new_line" data-linenumber="636" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

636

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<pre style="margin: 0;"> <span id="LC636" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">CTsStats</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">calcSampleStats</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">,</span><span class="n" style="color: #333;">CTs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

637

</td>

<td class="diff-line-num new_line" data-linenumber="637" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

637

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<pre style="margin: 0;"> <span id="LC637" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">GAsStats</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">calcSampleStats</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">,</span><span class="n" style="color: #333;">GAs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

638

</td>

<td class="diff-line-num new_line old" data-linenumber="638" style="width: 35px; color: rgba(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="LC638" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">REsStats</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">calcSampleStats</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">,</span><span class="n" style="color: #333;">REs</span><span class="p">)</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="638" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

638

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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="LC638" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">REsStats</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">calcSampleStats</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">,</span><span class="n" style="color: #333;">REs</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

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<td class="diff-line-num new_line" data-linenumber="639" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

639

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<pre style="margin: 0;"> <span id="LC639" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Plotting the posterior predictive intervals</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

640

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<td class="diff-line-num new_line" data-linenumber="640" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

640

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<pre style="margin: 0;"> <span id="LC640" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">ggplot</span><span class="p">()</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

641

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<td class="diff-line-num new_line old" data-linenumber="641" style="width: 35px; color: rgba(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="LC641" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_point</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">mea</span><span class="p">,</span><span class="n" style="color: #333;">colour</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"C->T"</span><span class="p"><span class="idiff left">,</span></span><span class="n" style="color: #333;"><span class="idiff">aes_string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"subs"</span></span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CTsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="641" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

641

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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="LC641" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_point</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">mea</span><span class="p">,</span><span class="n" style="color: #333;">colour</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"C->T"</span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CTsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

642

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<td class="diff-line-num new_line" data-linenumber="642" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

642

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

<pre style="margin: 0;"> <span id="LC642" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_point</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">mea</span><span class="p">,</span><span class="n" style="color: #333;">colour</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"G->A"</span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">GAsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

643

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<td class="diff-line-num new_line" data-linenumber="643" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

643

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

<pre style="margin: 0;"> <span id="LC643" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_point</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">mea</span><span class="p">,</span><span class="n" style="color: #333;">colour</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Others"</span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">REsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="644" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

644

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<td class="diff-line-num new_line old" data-linenumber="644" style="width: 35px; color: rgba(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="LC644" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_errorbar</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="n" style="color: #333;"><span class="idiff">med</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">y</span>min</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loCI</span><span class="p">,</span><span class="n" style="color: #333;">ymax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">hiCI</span><span class="p">,</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"C->T"</span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CTsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

645

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<td class="diff-line-num new_line old" data-linenumber="644" style="width: 35px; color: rgba(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="LC645" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_errorbar</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="n" style="color: #333;"><span class="idiff">med</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">y</span>min</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loCI</span><span class="p">,</span><span class="n" style="color: #333;">ymax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">hiCI</span><span class="p">,</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"G->A"</span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">GAsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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646

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<pre style="margin: 0;">-<span id="LC646" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_errorbar</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">y</span><span class="o" style="font-weight: 600;"><span class="idiff left">=</span></span><span class="n" style="color: #333;"><span class="idiff">med</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff right">y</span>min</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loCI</span><span class="p">,</span><span class="n" style="color: #333;">ymax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">hiCI</span><span class="p">,</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Others"</span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">REsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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644

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<pre style="margin: 0;">+<span id="LC644" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_errorbar</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">ymin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loCI</span><span class="p">,</span><span class="n" style="color: #333;">ymax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">hiCI</span><span class="p">,</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"C->T"</span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">CTsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="645" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

645

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<pre style="margin: 0;">+<span id="LC645" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_errorbar</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">ymin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loCI</span><span class="p">,</span><span class="n" style="color: #333;">ymax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">hiCI</span><span class="p">,</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"G->A"</span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">GAsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="646" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

646

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<pre style="margin: 0;">+<span id="LC646" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_errorbar</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">x</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">x</span><span class="p">,</span><span class="n" style="color: #333;">ymin</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loCI</span><span class="p">,</span><span class="n" style="color: #333;">ymax</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">hiCI</span><span class="p">,</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"Others"</span><span class="p">),</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">REsStats</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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647

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<td class="diff-line-num new_line" data-linenumber="647" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

647

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<pre style="margin: 0;"> <span id="LC647" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_line</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">oneBased</span><span class="p">,</span><span class="n" style="color: #333;">C.T</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">C</span><span class="p">),</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"red"</span><span class="p">,</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">data.frame</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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648

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<td class="diff-line-num new_line" data-linenumber="648" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

648

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<pre style="margin: 0;"> <span id="LC648" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_line</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">oneBased</span><span class="p">,</span><span class="n" style="color: #333;">G.A</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">G</span><span class="p">),</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"green"</span><span class="p">,</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">data.frame</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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649

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649

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<pre style="margin: 0;"> <span id="LC649" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;">geom_line</span><span class="p">(</span><span class="n" style="color: #333;">aes</span><span class="p">(</span><span class="n" style="color: #333;">oneBased</span><span class="p">,((</span><span class="n" style="color: #333;">A.C</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">A.G</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">A.T</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">A</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="n" style="color: #333;">C.A</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">C.G</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">C</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="n" style="color: #333;">G.C</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">G.T</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">G</span><span class="o" style="font-weight: 600;">+</span><span class="p">(</span><span class="nb" style="color: #0086b3;">T</span><span class="n" style="color: #333;">.A</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">T</span><span class="n" style="color: #333;">.C</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">T</span><span class="n" style="color: #333;">.G</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="nb" style="color: #0086b3;">T</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="m" style="color: #099;">10</span><span class="p">),</span><span class="n" style="color: #333;">color</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">"blue"</span><span class="p">,</span><span class="n" style="color: #333;">data</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">data.frame</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">))</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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650

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<td class="diff-line-num new_line old" data-linenumber="650" style="width: 35px; color: rgba(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="LC650" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;"><span class="idiff left">ylab</span></span><span class="p"><span class="idiff">(</span></span><span class="s2" style="color: #d14;"><span class="idiff">"Substitution rate"</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span></span>

</pre>

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651

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<pre style="margin: 0;">-<span id="LC651" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;"><span class="idiff left">xlab</span></span><span class="p"><span class="idiff">(</span></span><span class="s2" style="color: #d14;"><span class="idiff">"Relative position"</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span></span>

</pre>

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652

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<pre style="margin: 0;">-<span id="LC652" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;"><span class="idiff left">scale_x_continuous</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">breaks</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">bres</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">labels</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">labs</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">+</span></span></span>

</pre>

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653

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<td class="diff-line-num new_line old" data-linenumber="650" style="width: 35px; color: rgba(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="LC653" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;"><span class="idiff left">labs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">colour</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="s2" style="color: #d14;"><span class="idiff right">"Subs. type</span>"</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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654

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<td class="diff-line-num new_line old" data-linenumber="650" style="width: 35px; color: rgba(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="LC654" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;"><span class="idiff left">ggtitle</span></span><span class="p"><span class="idiff">(</span></span><span class="s2" style="color: #d14;"><span class="idiff right">"Posterior prediction intervals"</span></span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="650" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

650

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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="LC650" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;"><span class="idiff left">labs</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">y</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="s2" style="color: #d14;"><span class="idiff">"Substitution rate"</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="651" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

651

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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="LC651" class="line" lang="r"><span class="w" style="color: #bbb;">         <span class="idiff left">     </span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="s2" style="color: #d14;"><span class="idiff">"Relative position"</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="652" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

652

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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="LC652" class="line" lang="r"><span class="w" style="color: #bbb;">         <span class="idiff left">     </span></span><span class="n" style="color: #333;"><span class="idiff">colour</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="s2" style="color: #d14;"><span class="idiff">"Subs. type"</span></span><span class="p"><span class="idiff right">,</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="653" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

653

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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="LC653" class="line" lang="r"><span class="w" style="color: #bbb;">         <span class="idiff left">     </span></span><span class="n" style="color: #333;"><span class="idiff">title</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="s2" style="color: #d14;"><span class="idiff right">"Posterior prediction intervals</span>"</span><span class="p">)</span><span class="o" style="font-weight: 600;">+</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="654" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

654

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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="LC654" class="line" lang="r"><span class="w" style="color: #bbb;">         </span><span class="n" style="color: #333;"><span class="idiff left">scale_x_continuous</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">breaks</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff">bres</span></span><span class="p"><span class="idiff">,</span></span><span class="n" style="color: #333;"><span class="idiff">labels</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="n" style="color: #333;"><span class="idiff right">labs</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

655

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<td class="diff-line-num new_line" data-linenumber="655" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

655

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

<pre style="margin: 0;"> <span id="LC655" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">output</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">use_bw_theme</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

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<td class="diff-line-num new_line" data-linenumber="656" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

656

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<pre style="margin: 0;"> <span id="LC656" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">p</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">p</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">theme_bw</span><span class="p">()</span></span>

</pre>

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657

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<td class="diff-line-num new_line" data-linenumber="657" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

657

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<pre style="margin: 0;"> <span id="LC657" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

658

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<td class="diff-line-num new_line" data-linenumber="658" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

658

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

<pre style="margin: 0;"> <span id="LC658" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">plot</span><span class="p">(</span><span class="n" style="color: #333;">p</span><span class="p">)</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

659

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<td class="diff-line-num new_line old" data-linenumber="659" style="width: 35px; color: rgba(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="LC659" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#The correcting probabilities<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="659" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

659

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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="LC659" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#The correcting probabilities</span></span>

</pre>

</td>

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660

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<td class="diff-line-num new_line" data-linenumber="660" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

660

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

<pre style="margin: 0;"> <span id="LC660" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">coProbs</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cbind</span><span class="p">(</span><span class="n" style="color: #333;">da</span><span class="p">[,</span><span class="s2" style="color: #d14;">"Pos"</span><span class="p">],</span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">C</span><span class="m" style="color: #099;">2</span><span class="n" style="color: #333;">TProbs</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">mean</span><span class="p">),</span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">G</span><span class="m" style="color: #099;">2</span><span class="n" style="color: #333;">AProbs</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">mean</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

661

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<td class="diff-line-num new_line" data-linenumber="661" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

661

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

<pre style="margin: 0;"> <span id="LC661" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">colnames</span><span class="p">(</span><span class="n" style="color: #333;">coProbs</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="s2" style="color: #d14;">"Position"</span><span class="p">,</span><span class="s2" style="color: #d14;">"C.T"</span><span class="p">,</span><span class="s2" style="color: #d14;">"G.A"</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC662" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="nf" style="color: #900; font-weight: 600;">return</span><span class="p">(</span><span class="n" style="color: #333;">coProbs</span><span class="p">)</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -686,9 +686,8 @@ writeMCMC <- function(out,filename){</td>

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<pre style="margin: 0;"> <span id="LC686" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">qua</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">out</span><span class="p">[,</span><span class="n" style="color: #333;">parameters</span><span class="p">],</span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="n" style="color: #333;">quantile</span><span class="p">,</span><span class="n" style="color: #333;">seq</span><span class="p">(</span><span class="n" style="color: #333;">from</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">to</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">by</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">.025</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC687" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">acc</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">out</span><span class="p">[,</span><span class="n" style="color: #333;">parameters</span><span class="p">],</span><span class="m" style="color: #099;">2</span><span class="p">,</span><span class="n" style="color: #333;">accRat</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC688" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">summStat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">rbind</span><span class="p">(</span><span class="n" style="color: #333;">mea</span><span class="p">,</span><span class="n" style="color: #333;">std</span><span class="p">,</span><span class="n" style="color: #333;">acc</span><span class="p">,</span><span class="n" style="color: #333;">qua</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="689" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC689" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">rownames</span><span class="p">(</span><span class="n" style="color: #333;">summStat</span><span class="p">)[</span><span class="m" style="color: #099;">1</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Mean"</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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<td class="diff-line-num new_line old" data-linenumber="689" style="width: 35px; color: rgba(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="LC690" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">rownames</span><span class="p">(</span><span class="n" style="color: #333;">summStat</span><span class="p">)[</span><span class="m" style="color: #099;">2</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Std."</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="689" style="width: 35px; color: rgba(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="LC691" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">rownames</span><span class="p">(</span><span class="n" style="color: #333;">summStat</span><span class="p">)[</span><span class="m" style="color: #099;">3</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Acceptance ratio"</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC689" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">rownames</span><span class="p">(</span><span class="n" style="color: #333;">summStat</span><span class="p">)[</span><span class="m" style="color: #099;">1</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Mean"</span></span>

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<td class="diff-line-num new old_line" data-linenumber="692" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="690" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC690" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">rownames</span><span class="p">(</span><span class="n" style="color: #333;">summStat</span><span class="p">)[</span><span class="m" style="color: #099;">2</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Std."</span></span>

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<pre style="margin: 0;">+<span id="LC691" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">rownames</span><span class="p">(</span><span class="n" style="color: #333;">summStat</span><span class="p">)[</span><span class="m" style="color: #099;">3</span><span class="p">]</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Acceptance ratio"</span></span>

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<pre style="margin: 0;"> <span id="LC692" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">write.csv</span><span class="p">(</span><span class="n" style="color: #333;">summStat</span><span class="p">,</span><span class="n" style="color: #333;">paste</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span><span class="s2" style="color: #d14;">"_summ_stat.csv"</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC693" class="line" lang="r"><span class="p">}</span></span></pre>

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<pre style="margin: 0;">-<span id="LC694" class="line" lang="r"></span></pre>

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<li id="107569f6853a50f9e86ad7b15639ea4b3fd398b4">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#107569f6853a50f9e86ad7b15639ea4b3fd398b4"><strong>mapdamage/Rscripts/stats/main.R</strong></a>

<hr>

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#The main work flow of the package</span></span>

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2

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2

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#Load the libraries</span></span>

</pre>

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

3

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

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="r"><span class="n" style="color: #333;">suppress<span class="idiff left">Messages</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">library</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">inline</span></span><span class="p"><span class="idiff">))</span></span><span class="w" style="color: #bbb;"><span class="idiff">  </span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#Already checked the libraries </span></span></span>

</pre>

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

4

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

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="r"><span class="n" style="color: #333;">suppressMessages</span><span class="p">(</span><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">ggplot2</span><span class="p">))</span><span class="w" style="color: #bbb;"> </span><span class="c1" style="color: #998; font-style: italic;">#thus ignoring any messages from them</span></span>

</pre>

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

5

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="r"><span class="n" style="color: #333;">suppressMessages</span><span class="p">(</span><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">Rcpp</span><span class="p">))</span></span>

</pre>

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

6

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

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="r"><span class="n" style="color: #333;">suppress<span class="idiff left">Messages</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">library</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gam</span></span><span class="p"><span class="idiff">))</span></span><span class="w" style="color: #bbb;"><span class="idiff right"> </span></span></span>

</pre>

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

7

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

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="r"><span class="n" style="color: #333;">suppressMessages</span><span class="p">(</span><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">RcppGSL</span><span class="p">))</span></span>

</pre>

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

</td>

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

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="r"><span class="n" style="color: #333;">suppress<span class="idiff left">PackageStartupMessages</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">library</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">inline</span></span><span class="p"><span class="idiff">))</span></span><span class="w" style="color: #bbb;"><span class="idiff">  </span></span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">#Already checked the libraries</span></span></span>

</pre>

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

</td>

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

4

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

<pre style="margin: 0;">+<span id="LC4" class="line" lang="r"><span class="n" style="color: #333;">suppress<span class="idiff left right">PackageStartup</span>Messages</span><span class="p">(</span><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">ggplot2</span><span class="p">))</span><span class="w" style="color: #bbb;"> </span><span class="c1" style="color: #998; font-style: italic;">#thus ignoring any messages from them</span></span>

</pre>

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

</td>

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

5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="r"><span class="n" style="color: #333;">suppress<span class="idiff left right">PackageStartup</span>Messages</span><span class="p">(</span><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">Rcpp</span><span class="p">))</span></span>

</pre>

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

</td>

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

6

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="r"><span class="n" style="color: #333;">suppress<span class="idiff left">PackageStartupMessages</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">library</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">gam</span></span><span class="p"><span class="idiff right">))</span></span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="r"><span class="n" style="color: #333;">suppress<span class="idiff left right">PackageStartup</span>Messages</span><span class="p">(</span><span class="n" style="color: #333;">library</span><span class="p">(</span><span class="n" style="color: #333;">RcppGSL</span><span class="p">))</span></span>

</pre>

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

8

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

</pre>

</td>

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

9

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

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#Miscellaneous functions<span class="idiff left right"> </span></span></span>

</pre>

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

</td>

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

9

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#Miscellaneous functions</span></span>

</pre>

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

10

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

10

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="r"><span class="n" style="color: #333;">source</span><span class="p">(</span><span class="n" style="color: #333;">paste</span><span class="p">(</span><span class="n" style="color: #333;">path_to_mapDamage_stats</span><span class="p">,</span><span class="s2" style="color: #d14;">"function.R"</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span><span class="p">))</span></span>

</pre>

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

11

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

11

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

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

</pre>

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

12

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

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#Prior and proposal distributions for the parameters</span></span>

</pre>

</td>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@ source(paste(path_to_mapDamage_stats,"postConditonal.R",sep=""))</td>

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

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#functions for the grid search</span></span>

</pre>

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

19

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

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="r"><span class="n" style="color: #333;">source</span><span class="p">(</span><span class="n" style="color: #333;">paste</span><span class="p">(</span><span class="n" style="color: #333;">path_to_mapDamage_stats</span><span class="p">,</span><span class="s2" style="color: #d14;">"start.R"</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span><span class="p">))</span></span>

</pre>

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

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

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

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#functions for loading the data<span class="idiff left right"> </span></span></span>

</pre>

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

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

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#functions for loading the data</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="r"><span class="n" style="color: #333;">source</span><span class="p">(</span><span class="n" style="color: #333;">paste</span><span class="p">(</span><span class="n" style="color: #333;">path_to_mapDamage_stats</span><span class="p">,</span><span class="s2" style="color: #d14;">"data.R"</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span><span class="p">))</span></span>

</pre>

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

23

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -39,14 +39,14 @@ if (forward_only && reverse_only){</td>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">stop</span><span class="p">()</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="r"><span class="p">}</span></span>

</pre>

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

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="r"><span class="n" style="color: #333;">fow_dat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="n" style="color: #333;">readMapDamData</span><span class="p">(</span><span class="n" style="color: #333;">path_to_dat</span><span class="p">)</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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="r"><span class="n" style="color: #333;">fow_dat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="n" style="color: #333;">readMapDamData</span><span class="p">(</span><span class="n" style="color: #333;">path_to_dat</span><span class="p">)</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="r"><span class="n" style="color: #333;">rev_dat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="n" style="color: #333;">readMapDamData</span><span class="p">(</span><span class="n" style="color: #333;">path_to_dat</span><span class="p">,</span><span class="n" style="color: #333;">forward</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">0</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="r"><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">forward_only</span><span class="p">){</span></span>

</pre>

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

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

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Taking only the forward part</span></span>

</pre>

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

46

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

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">dat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">fow_dat</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">sub_length</span><span class="p">,]</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">dat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">fow_dat</span><span class="p">[</span><span class="m" style="color: #099;">1</span><span class="o" style="font-weight: 600;">:</span><span class="n" style="color: #333;">sub_length</span><span class="p">,]</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="r"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">reverse_only</span><span class="p">){</span></span>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Taking only the reverse part</span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">dat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">rev_dat</span><span class="p">[</span><span class="n" style="color: #333;">sub_length</span><span class="o" style="font-weight: 600;">:</span><span class="m" style="color: #099;">1</span><span class="p">,]</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">dat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">rev_dat</span><span class="p">[</span><span class="n" style="color: #333;">sub_length</span><span class="o" style="font-weight: 600;">:</span><span class="m" style="color: #099;">1</span><span class="p">,]</span></span>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="r"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Using both ends</span></span>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">dat</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">joinFowAndRev</span><span class="p">(</span><span class="n" style="color: #333;">fow_dat</span><span class="p">,</span><span class="n" style="color: #333;">rev_dat</span><span class="p">,</span><span class="n" style="color: #333;">sub_length</span><span class="p">)</span></span>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -107,7 +107,7 @@ cu_pa$ThetaMat <- getPmat(cu_pa$Theta,cu_pa$Rho,cu_pa$acgt)</td>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="r"></span>

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

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#######################################################</span></span>

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

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC110" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#              Setting the lambda vector<span class="idiff left right"> </span></span></span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#              Setting the lambda vector</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC111" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;"> <span id="LC112" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#######################################################</span></span>

</pre>

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

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

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -127,17 +127,17 @@ if (!cu_pa$same_overhangs){</td>

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

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<pre style="margin: 0;"> <span id="LC128" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#######################################################</span></span>

</pre>

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129

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129

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<pre style="margin: 0;"> <span id="LC129" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="130" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

130

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<td class="diff-line-num new_line old" data-linenumber="130" style="width: 35px; color: rgba(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="LC130" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#              Setting the nu vector<span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#              Setting the nu vector</span></span>

</pre>

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131

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131

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<pre style="margin: 0;"> <span id="LC131" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<td class="diff-line-num old_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

132

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<pre style="margin: 0;"> <span id="LC132" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#######################################################</span></span>

</pre>

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133

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133

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<pre style="margin: 0;"> <span id="LC133" class="line" lang="r"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="r"><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">ds_protocol</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">&</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">nuSamples</span><span class="o" style="font-weight: 600;">!=</span><span class="m" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

135

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<td class="diff-line-num new_line old" data-linenumber="135" style="width: 35px; color: rgba(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="LC135" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Using the single stranded protocol with nu samples which makes<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="135" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC135" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Using the single stranded protocol with nu samples which makes</span></span>

</pre>

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

136

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

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#no sense</span></span>

</pre>

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

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s2" style="color: #d14;">"Silly to use the MC estimation for nu_i if using the single stranded protocol"</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">stderr</span><span class="p">())</span></span>

</pre>

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138

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

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">stop</span><span class="p">()</span></span>

</pre>

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

139

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

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="r"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">nuSamples</span><span class="o" style="font-weight: 600;">!=</span><span class="m" style="color: #099;">0</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">&</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">fix_nu</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

140

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<td class="diff-line-num new_line old" data-linenumber="140" style="width: 35px; color: rgba(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="LC140" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Using the fixed nu parameter with nu samples which makes no sense<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC140" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Using the fixed nu parameter with nu samples which makes no sense</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<td class="diff-line-num new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

141

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s2" style="color: #d14;">"Silly to use the MC estimation for nu_i and use fix_nu "</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">stderr</span><span class="p">())</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<td class="diff-line-num new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

142

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">stop</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="r"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">nuSamples</span><span class="o" style="font-weight: 600;">!=</span><span class="m" style="color: #099;">0</span><span class="p">){</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -164,7 +164,7 @@ if (!cu_pa$ds_protocol & cu_pa$nuSamples!=0){</td>

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164

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">nuVec</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">rep</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="m" style="color: #099;">2</span><span class="p">),</span><span class="nf" style="color: #900; font-weight: 600;">rep</span><span class="p">(</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="m" style="color: #099;">2</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="r"><span class="p">}</span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#This is for a non linear nick frequency, assumes the G>T and G>A are<span class="idiff left right"> </span></span></span>

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<td class="diff-line-num new old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC167" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#This is for a non linear nick frequency, assumes the G>T and G>A are</span></span>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#mostly due to DNA damage patterns do not use for low damage datasets</span></span>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">te</span><span class="o" style="font-weight: 600;"><-</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"C.T"</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">])</span><span class="o" style="font-weight: 600;">/</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G.A"</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"G"</span><span class="p">]</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"C.T"</span><span class="p">]</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333;">dat</span><span class="p">[,</span><span class="s2" style="color: #d14;">"C"</span><span class="p">])</span></span>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">sum</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">is.na</span><span class="p">(</span><span class="n" style="color: #333;">te</span><span class="p">)</span><span class="w" style="color: #bbb;"> </span><span class="p">)</span><span class="o" style="font-weight: 600;">!=</span><span class="m" style="color: #099;">0</span><span class="w" style="color: #bbb;"> </span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -177,7 +177,7 @@ if (!cu_pa$ds_protocol & cu_pa$nuSamples!=0){</td>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="r"><span class="w" style="color: #bbb;">            </span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">nuVec</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">rep</span><span class="p">(</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="m" style="color: #099;">2</span><span class="p">),</span><span class="nf" style="color: #900; font-weight: 600;">rep</span><span class="p">(</span><span class="m" style="color: #099;">0</span><span class="p">,</span><span class="n" style="color: #333;">nrow</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">)</span><span class="o" style="font-weight: 600;">/</span><span class="m" style="color: #099;">2</span><span class="p">))</span></span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="p">}</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC180" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#The substitutes seem to be okay estimate the nick frequency using GAM<span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="c1" style="color: #998; font-style: italic;">#The substitutes seem to be okay estimate the nick frequency using GAM</span></span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="r"><span class="w" style="color: #bbb;">        </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">forward_only</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;">||</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">reverse_only</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="r"><span class="w" style="color: #bbb;">            </span><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">use_raw_nick_freq</span><span class="p">){</span></span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="r"><span class="w" style="color: #bbb;">                </span><span class="c1" style="color: #998; font-style: italic;">#Use the frequency</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -202,14 +202,14 @@ if (!cu_pa$ds_protocol & cu_pa$nuSamples!=0){</td>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="r"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#######################################################</span></span>

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<td class="diff-line-num old old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC205" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#          Finding an "optimal" starting place<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC205" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#          Finding an "optimal" starting place</span></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#######################################################</span></span>

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<pre style="margin: 0;"> <span id="LC208" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC209" class="line" lang="r"><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">grid_iter</span><span class="o" style="font-weight: 600;">!=</span><span class="m" style="color: #099;">0</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="210" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC210" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Start at random places and optimize the likelihood function</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">cu_pa</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">gridSearch</span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="p">,</span><span class="n" style="color: #333;">grid_iter</span><span class="p">)</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC212" class="line" lang="r"><span class="p">}</span><span class="w" style="color: #bbb;"><span class="idiff left right"> </span></span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC211" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">cu_pa</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">gridSearch</span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="p">,</span><span class="n" style="color: #333;">grid_iter</span><span class="p">)</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC212" class="line" lang="r"><span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC213" class="line" lang="r"></span>

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<pre style="margin: 0;"> <span id="LC214" class="line" lang="r"><span class="c1" style="color: #998; font-style: italic;">#Calculate the log likelihood in the beginning</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="215" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

215

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<pre style="margin: 0;"> <span id="LC215" class="line" lang="r"><span class="k" style="font-weight: 600;">if</span><span class="w" style="color: #bbb;"> </span><span class="p">(</span><span class="n" style="color: #333;">cu_pa</span><span class="o" style="font-weight: 600;">$</span><span class="n" style="color: #333;">same_overhangs</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -267,11 +267,11 @@ if (out_file_base!=""){</td>

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<td class="diff-line-num old_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC267" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">pdf</span><span class="p">(</span><span class="n" style="color: #333;">paste</span><span class="p">(</span><span class="n" style="color: #333;">out_file_base</span><span class="p">,</span><span class="s2" style="color: #d14;">"_MCMC_hist.pdf"</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC268" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">plotEverything</span><span class="p">(</span><span class="n" style="color: #333;">mcmcOut</span><span class="p">,</span><span class="n" style="color: #333;">hi</span><span class="o" style="font-weight: 600;">=</span><span class="m" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC269" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">dev.off</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC270" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Posterior predictive plot<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="270" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC270" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Posterior predictive plot</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC271" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">pdf</span><span class="p">(</span><span class="n" style="color: #333;">paste</span><span class="p">(</span><span class="n" style="color: #333;">out_file_base</span><span class="p">,</span><span class="s2" style="color: #d14;">"_MCMC_post_pred.pdf"</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC272" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">siteProb</span><span class="w" style="color: #bbb;"> </span><span class="o" style="font-weight: 600;"><-</span><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">postPredCheck</span><span class="p">(</span><span class="n" style="color: #333;">dat</span><span class="p">,</span><span class="n" style="color: #333;">mcmcOut</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC273" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">dev.off</span><span class="p">()</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="274" style="width: 35px; color: rgba(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="LC274" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Write correcting probabilities<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC274" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="c1" style="color: #998; font-style: italic;">#Write correcting probabilities</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">write.csv</span><span class="p">(</span><span class="n" style="color: #333;">siteProb</span><span class="p">,</span><span class="n" style="color: #333;">paste</span><span class="p">(</span><span class="n" style="color: #333;">out_file_base</span><span class="p">,</span><span class="s2" style="color: #d14;">"_MCMC_correct_prob.csv"</span><span class="p">,</span><span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s2" style="color: #d14;">""</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="r"><span class="p">}</span><span class="w" style="color: #bbb;"> </span><span class="k" style="font-weight: 600;">else</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="r"><span class="w" style="color: #bbb;">    </span><span class="n" style="color: #333;">cat</span><span class="p">(</span><span class="s2" style="color: #d14;">"Plotting\n"</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="a42a42a3de2ad00a1423a75f0791ae4dd1737b53">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#a42a42a3de2ad00a1423a75f0791ae4dd1737b53"><strong>mapdamage/__init__.py</strong></a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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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 class="idiff left right">3</span></span></span>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">mapdamage.parseoptions</span></span>

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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;">mapdamage.seq</span></span>

</pre>

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<br>

</li>

<li id="4481def45a752330bb6f29dd87ff5a798f79aeb2">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#4481def45a752330bb6f29dd87ff5a798f79aeb2"><strong>mapdamage/align.py</strong></a>

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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>

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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;">itertools</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;">mapdamage</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -16,11 +14,11 @@ import mapdamage</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#X 8 sequence mismatch</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_coordinates</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">):</span><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_coordinates</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">  <span class="s" style="color: #d14;">""" return external coordinates of aligned read bases """</span></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">  <span class="n" style="color: #333;">fivep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aend</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_reverse</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">  <span class="n" style="color: #333;">threep</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_reverse</span> <span class="k" style="font-weight: 600;">else</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">aend</span></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">fivep</span><span class="p">,</span> <span class="n" style="color: #333;">threep</span></span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -41,9 +39,9 @@ def get_around(coord, chrom, reflengths, length, ref):</td>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">align</span><span class="p">(</span><span class="n" style="color: #333;">cigarlist</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="python">  <span class="s" style="color: #d14;">""" insert gaps according to the cigar string<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"><span class="s" style="color: #d14;">  deletion: gaps to be inserted into read sequences,<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="s" style="color: #d14;">  insertions: gaps to be inserted into reference sequence """</span><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python">  <span class="s" style="color: #d14;">""" insert gaps according to the cigar string</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"><span class="s" style="color: #d14;">  deletion: gaps to be inserted into read sequences,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"><span class="s" style="color: #d14;">  insertions: gaps to be inserted into reference sequence """</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python">  <span class="n" style="color: #333;">lref</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nbr</span><span class="p">,</span> <span class="n" style="color: #333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parse_cigar</span><span class="p">(</span><span class="n" style="color: #333;">cigarlist</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python">    <span class="n" style="color: #333;">lref</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">:</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"-"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nbr</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -56,9 +54,9 @@ def align(cigarlist, seq, ref):</td>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">align_with_qual</span><span class="p">(</span><span class="n" style="color: #333;">cigarlist</span><span class="p">,</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">,</span> <span class="n" style="color: #333;">threshold</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="python">  <span class="s" style="color: #d14;">""" insert gaps according to the cigar string<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;">  deletion: gaps to be inserted into read sequences and qualities,<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python"><span class="s" style="color: #d14;">  insertions: gaps to be inserted into reference sequence """</span><span class="idiff left right">  </span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python">  <span class="s" style="color: #d14;">""" insert gaps according to the cigar string</span></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;">  deletion: gaps to be inserted into read sequences and qualities,</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python"><span class="s" style="color: #d14;">  insertions: gaps to be inserted into reference sequence """</span></span>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python">  <span class="n" style="color: #333;">lref</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">nbr</span><span class="p">,</span> <span class="n" style="color: #333;">idx</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">parse_cigar</span><span class="p">(</span><span class="n" style="color: #333;">cigarlist</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="LC62" class="line" lang="python">    <span class="n" style="color: #333;">lref</span><span class="p">[</span><span class="n" style="color: #333;">idx</span><span class="p">:</span><span class="n" style="color: #333;">idx</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"-"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">nbr</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -84,7 +82,7 @@ def get_mis(read, seq, refseq, ref, length, tab, end):</td>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="python">  <span class="n" style="color: #333;">std</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_reverse</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'+'</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">  <span class="n" style="color: #333;">subtable</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tab</span><span class="p">[</span><span class="n" style="color: #333;">ref</span><span class="p">][</span><span class="n" style="color: #333;">end</span><span class="p">][</span><span class="n" style="color: #333;">std</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">nt_seq</span><span class="p">,</span> <span class="n" style="color: #333;">nt_ref</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">itertools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">izip</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">x</span>range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">),</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">refseq</span><span class="p">):</span></span>

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<pre style="margin: 0;">+<span id="LC85" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">nt_seq</span><span class="p">,</span> <span class="n" style="color: #333;">nt_ref</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">zip</span></span><span class="p"><span class="idiff right">(</span></span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">),</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">refseq</span><span class="p">):</span></span>

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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;">nt_seq</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"ACGT-"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">nt_ref</span> <span class="ow" style="font-weight: 600;">in</span> <span class="s" style="color: #d14;">"ACGT-"</span><span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">      <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nt_ref</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"-"</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># record base composition in the reference, only A, C, G, T</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -106,7 +104,7 @@ def parse_cigar(cigarlist, ope):</td>

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<td class="diff-line-num old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">operation</span><span class="p">,</span> <span class="n" style="color: #333;">length</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">cigarlist</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">operation</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">ope</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">        <span class="n" style="color: #333;">coordinate</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">append</span><span class="p">([</span><span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">tlength</span><span class="p">])</span></span>

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<pre style="margin: 0;">-<span id="LC109" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">operation</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">oplist</span><span class="p">:</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">operation</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">oplist</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">        <span class="n" style="color: #333;">tlength</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">length</span></span>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">coordinate</span></span>

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -127,8 +125,3 @@ def record_soft_clipping(read, tab, length):</td>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="python">      <span class="n" style="color: #333;">end</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'5p'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_reverse</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'3p'</span></span>

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<td class="diff-line-num new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="python">    <span class="n" style="color: #333;">update_table</span><span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">nbases</span><span class="p">)</span></span></pre>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="python"></span></pre>

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<li id="401cd204f5537ece913ab718c203d3b6c6248caa">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#401cd204f5537ece913ab718c203d3b6c6248caa"><strong>mapdamage/composition.py</strong></a>

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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>

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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;">mapdamage</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;">itertools</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;">csv</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,8 +8,8 @@ def count_ref_comp(read, chrom, before, after, comp):</td>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python">  <span class="s" style="color: #d14;">""" record basae composition in external genomic regions """</span></span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python">  <span class="n" style="color: #333;">std</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_reverse</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'+'</span></span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python">  <span class="n" style="color: #333;">_update_table</span><span class="p">(</span><span class="n" style="color: #333;">comp</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">][</span><span class="s" style="color: #d14;">'5p'</span><span class="p">][</span><span class="n" style="color: #333;">std</span><span class="p">],</span> <span class="n" style="color: #333;">before</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">before</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="LC14" class="line" lang="python">  <span class="n" style="color: #333;">_update_table</span><span class="p">(</span><span class="n" style="color: #333;">comp</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">][</span><span class="s" style="color: #d14;">'3p'</span><span class="p">][</span><span class="n" style="color: #333;">std</span><span class="p">],</span> <span class="n" style="color: #333;">after</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">after</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="LC11" class="line" lang="python">  <span class="n" style="color: #333;">_update_table</span><span class="p">(</span><span class="n" style="color: #333;">comp</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">][</span><span class="s" style="color: #d14;">'5p'</span><span class="p">][</span><span class="n" style="color: #333;">std</span><span class="p">],</span> <span class="n" style="color: #333;">before</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">before</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="LC12" class="line" lang="python">  <span class="n" style="color: #333;">_update_table</span><span class="p">(</span><span class="n" style="color: #333;">comp</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">][</span><span class="s" style="color: #d14;">'3p'</span><span class="p">][</span><span class="n" style="color: #333;">std</span><span class="p">],</span> <span class="n" style="color: #333;">after</span><span class="p">,</span>  <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">after</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="LC13" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">count_read_comp</span><span class="p">(</span><span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">chrom</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">,</span> <span class="n" style="color: #333;">comp</span><span class="p">):</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,12 +18,12 @@ def count_read_comp(read, chrom, length, comp):</td>

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<td class="diff-line-num old_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python">  <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_reverse</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">    <span class="n" style="color: #333;">std</span><span class="p">,</span> <span class="n" style="color: #333;">seq</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;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">revcomp</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python">  <span class="n" style="color: #333;">_update_table</span><span class="p">(</span><span class="n" style="color: #333;">comp</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">][</span><span class="s" style="color: #d14;">'5p'</span><span class="p">][</span><span class="n" style="color: #333;">std</span><span class="p">],</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span>           <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line 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">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python">  <span class="n" style="color: #333;">_update_table</span><span class="p">(</span><span class="n" style="color: #333;">comp</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">][</span><span class="s" style="color: #d14;">'3p'</span><span class="p">][</span><span class="n" style="color: #333;">std</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">reversed</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">),</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</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="n" style="color: #333;">length</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="mi" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python">  <span class="n" style="color: #333;">_update_table</span><span class="p">(</span><span class="n" style="color: #333;">comp</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">][</span><span class="s" style="color: #d14;">'5p'</span><span class="p">][</span><span class="n" style="color: #333;">std</span><span class="p">],</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span>           <span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new old_line" 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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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python">  <span class="n" style="color: #333;">_update_table</span><span class="p">(</span><span class="n" style="color: #333;">comp</span><span class="p">[</span><span class="n" style="color: #333;">chrom</span><span class="p">][</span><span class="s" style="color: #d14;">'3p'</span><span class="p">][</span><span class="n" style="color: #333;">std</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">reversed</span><span class="p">(</span><span class="n" style="color: #333;">seq</span><span class="p">),</span> <span class="nb" style="color: #0086b3;">range</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="n" style="color: #333;">length</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="mi" style="color: #099;">1</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">_update_table</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">,</span> <span class="n" style="color: #333;">indices</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">nt</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">itertools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">i</span>zip</span><span class="p">(</span><span class="n" style="color: #333;">indices</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" 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;">for</span> <span class="p">(</span><span class="n" style="color: #333;">index</span><span class="p">,</span> <span class="n" style="color: #333;">nt</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">indices</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nt</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">table</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python">      <span class="n" style="color: #333;">table</span><span class="p">[</span><span class="n" style="color: #333;">nt</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

31

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,7 +33,7 @@ def get_base_comp(filename,destination=False):</td>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;">    Gets the basecomposition of all the sequences in filename</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python"><span class="s" style="color: #d14;">    and returns the value to destination if given.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python">    <span class="n" style="color: #333;">path_to_seqtk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rscript</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">construct_path</span><span class="p">(</span><span class="s" style="color: #d14;">"seqtk"</span><span class="p">,</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"seqtk"</span><span class="p">)</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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;">path_to_seqtk</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rscript</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">construct_path</span><span class="p">(</span><span class="s" style="color: #d14;">"seqtk"</span><span class="p">,</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"seqtk"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python">    <span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"A"</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"C"</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"G"</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">,</span><span class="s" style="color: #d14;">"T"</span><span class="p">:</span><span class="mi" style="color: #099;">0</span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

40

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python">    <span class="n" style="color: #333;">alp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span><span class="s" style="color: #d14;">"C"</span><span class="p">,</span><span class="s" style="color: #d14;">"G"</span><span class="p">,</span><span class="s" style="color: #d14;">"T"</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python">    <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,7 +45,7 @@ def get_base_comp(filename,destination=False):</td>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python">            <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="s" style="color: #d14;">"C"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="s" style="color: #d14;">"C"</span><span class="p">]</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;">tabs</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">            <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="s" style="color: #d14;">"G"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="s" style="color: #d14;">"G"</span><span class="p">]</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;">tabs</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="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python">            <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="s" style="color: #d14;">"T"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bases</span><span class="p">[</span><span class="s" style="color: #d14;">"T"</span><span class="p">]</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;">tabs</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">])</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">OSError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)<span class="idiff left right">,</span></span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python">    <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">OSError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">ValueError</span><span class="p">)</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">as</span></span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="python">        <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Seqtk failed: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">error</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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># get the base frequencies</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,7 +73,7 @@ def read_base_comp(filename):</td>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">        <span class="n" style="color: #333;">lp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">li</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">()</span></span>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">first_line</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python">            <span class="n" style="color: #333;">header</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lp</span></span>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python">            <span class="n" style="color: #333;">first_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span><span class="idiff left right"> </span></span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">            <span class="n" style="color: #333;">first_line</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">False</span></span>

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<pre style="margin: 0;"> <span id="LC77" 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="LC78" class="line" lang="python">            <span class="n" style="color: #333;">body</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">lp</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">    <span class="n" style="color: #333;">bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<br>

</li>

<li id="88a1d21eb50ece62b8a9d89ea1dcbc165188579f">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#88a1d21eb50ece62b8a9d89ea1dcbc165188579f"><strong>mapdamage/parseoptions.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>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">optparse</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">OptionParser</span><span class="p">,</span> <span class="n" style="color: #333;">OptionGroup</span><span class="p">,</span> <span class="n" style="color: #333;">SUPPRESS_HELP</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;">os</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;">sys</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

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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">@@ -38,7 +36,7 @@ def check_py_version():</td>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">options</span><span class="p">():</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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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<td class="diff-line-num new new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC39" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">options</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python">    <span class="n" style="color: #333;">parser</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">OptionParser</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">prog [options] -i BAMfile -r reference.fasta</span><span class="se" style="color: #d14;">\n\n</span><span class="s" style="color: #d14;">Use option -h or --help for help"</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">__version__</span><span class="p">,</span> \</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python">            <span class="n" style="color: #333;">epilog</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"report bugs to aginolhac@snm.ku.dk, MSchubert@snm.ku.dk or jonsson.hakon@gmail.com"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -153,7 +151,7 @@ def options():</td>

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<pre style="margin: 0;"> <span id="LC151" 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;">check_py_version</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="154" style="width: 35px; color: rgba(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="LC156" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># if the user wants to check the R packages then do that before the option parsing<span class="idiff left right"> </span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC154" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># if the user wants to check the R packages then do that before the option parsing</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<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;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">check_R_packages</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">check_R_lib</span><span class="p">():</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -224,7 +222,7 @@ def options():</td>

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<td class="diff-line-num old_line" data-linenumber="224" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="222" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="225" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="223" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># check destination for rescaled bam</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC224" 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;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rescale_out</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rescale</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rescale_only</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if there are mulitiple bam files to rescale then pick first one as<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC225" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># if there are mulitiple bam files to rescale then pick first one as</span></span>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># the name of the rescaled file</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span><span class="p">,</span><span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC228" class="line" lang="python">            <span class="n" style="color: #333;">basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">basename</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">])</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="233" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -235,12 +233,12 @@ def options():</td>

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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">isdir</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC235" 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;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet</span> <span class="ow" style="font-weight: 600;">and</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plot_only</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC238" class="line" lang="python">            <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"Warning, </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s already exists"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">options</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">folder</span></span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="236" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC236" 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;"><span class="idiff">"Warning, </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s already exists"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">options</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">folder</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

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<td class="diff-line-num new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plot_only</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">file_exist</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/dnacomp.txt"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">file_exist</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/misincorporation.txt"</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">                <span class="n" style="color: #333;">parser</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">error</span><span class="p">(</span><span class="s" style="color: #d14;">'folder </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s is not a valid result folder'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<pre style="margin: 0;">-<span id="LC243" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0750</span><span class="p">)</span></span>

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<td class="diff-line-num new new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC241" class="line" lang="python">        <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="p">,</span> <span class="n" style="color: #333;">mode</span> <span class="o" style="font-weight: 600;">=</span> <span class="mo" style="color: #099;">0<span class="idiff left right">o</span>750</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">plot_only</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stats_only</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rescale_only</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python">            <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Error, </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s does not exist while plot/stats/rescale only was used</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python">            <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">None</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -279,4 +277,3 @@ def options():</td>

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<pre style="margin: 0;"> <span id="LC277" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC278" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC279" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">options</span></span></pre>

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<pre style="margin: 0;">-<span id="LC282" class="line" lang="python"></span></pre>

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<br>

</li>

<li id="a30b6a3b0ae4d9941d25e49d20f6a1a496380bc4">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#a30b6a3b0ae4d9941d25e49d20f6a1a496380bc4"><strong>mapdamage/rescale.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="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,14 +31,14 @@ def get_corr_prob(folder, rescale_length_5p, rescale_length_3p):</td>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">        <span class="n" style="color: #333;">fi_handle</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">csv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">DictReader</span><span class="p">(</span><span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">full_path</span><span class="p">))</span></span>

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">        <span class="n" style="color: #333;">corr_prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC33" 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_handle</span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">corr_prob</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">line</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"Position"</span></span><span class="p"><span class="idiff right">])</span>):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left">line</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"Position"</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">corr_prob</span></span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">                <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="s" style="color: #d14;">'This file has multiple position definitions </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s, line </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'</span> <span class="o" style="font-weight: 600;">%</span> \</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

36

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python">                    <span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">,</span> <span class="n" style="color: #333;">fi_handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">line_num</span><span class="p">,</span> <span class="n" style="color: #333;">corr_prob</span><span class="p">[</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="s" style="color: #d14;">"Position"</span><span class="p">]]))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python">                <span class="n" style="color: #333;">corr_prob</span><span class="p">[</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="s" style="color: #d14;">"Position"</span><span class="p">])]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'C.T'</span><span class="p">:</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="s" style="color: #d14;">"C.T"</span><span class="p">]),</span> <span class="s" style="color: #d14;">'G.A'</span><span class="p">:</span><span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">[</span><span class="s" style="color: #d14;">"G.A"</span><span class="p">])}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Exclude probabilities for positions outside of user-specified region</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">corr_prob</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">(</span>):</span></span>

</pre>

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<td class="diff-line-num new old_line" 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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<td class="diff-line-num new new_line" 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="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">corr_prob</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">keys</span></span><span class="p"><span class="idiff right">()</span>):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;"><</span> <span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">rescale_length_3p</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">rescale_length_5p</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python">                <span class="n" style="color: #333;">corr_prob</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -75,13 +75,13 @@ def corr_this_base(corr_prob, nt_seq, nt_ref, pos, length,direction="both"):</td>

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<td class="diff-line-num new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python">    <span class="n" style="color: #333;">back_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">-</span><span class="n" style="color: #333;">length</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="76" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># position from 3' end</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">corr_prob</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">pos</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" data-linenumber="78" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">pos</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">corr_prob</span></span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python">        <span class="n" style="color: #333;">p5_corr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">corr_prob</span><span class="p">[</span><span class="n" style="color: #333;">pos</span><span class="p">][</span><span class="n" style="color: #333;">subs</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># correction from 5' end</span></span>

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<pre style="margin: 0;"> <span id="LC81" 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="LC82" class="line" lang="python">        <span class="n" style="color: #333;">p5_corr</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python"></span>

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<td class="diff-line-num old old_line" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">corr_prob</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">back_pos</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<td class="diff-line-num new new_line" 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">

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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="n" style="color: #333;"><span class="idiff left">back_pos</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">corr_prob</span></span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="python">        <span class="n" style="color: #333;">p3_corr</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">corr_prob</span><span class="p">[</span><span class="n" style="color: #333;">back_pos</span><span class="p">][</span><span class="n" style="color: #333;">subs</span><span class="p">]</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># correction from 3' end</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="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">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -104,7 +104,7 @@ def corr_this_base(corr_prob, nt_seq, nt_ref, pos, length,direction="both"):</td>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">initialize_subs</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="python">    <span class="s" style="color: #d14;">"""Initialize a substitution table, to track the expected substitution counts"""</span></span>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python">    <span class="n" style="color: #333;">per_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">130</span></span><span class="p"><span class="idiff">),[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff right">130</span></span><span class="p">))</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="python">    <span class="n" style="color: #333;">per_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">zip</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">,</span></span><span class="mi" style="color: #099;"><span class="idiff">130</span></span><span class="p"><span class="idiff">)),[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="mi" style="color: #099;"><span class="idiff">130</span></span><span class="p"><span class="idiff right">)</span>))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">    <span class="n" style="color: #333;">subs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"CT-before"</span><span class="p">:</span><span class="n" style="color: #333;">per_qual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(),</span>\</span>

</pre>

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">            <span class="s" style="color: #d14;">"TC-before"</span><span class="p">:</span><span class="n" style="color: #333;">per_qual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(),</span>\</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="python">            <span class="s" style="color: #d14;">"GA-before"</span><span class="p">:</span><span class="n" style="color: #333;">per_qual</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">copy</span><span class="p">(),</span>\</span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -164,7 +164,7 @@ def qual_summary_subs(subs):</td>

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<td class="diff-line-num old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="python">            <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">qv</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="165" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="python">                <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">qv</span> <span class="o" style="font-weight: 600;">>=</span> <span class="n" style="color: #333;">lv</span> <span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="166" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python">                    <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"-Q"</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;">lv</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC167" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">subs</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">has_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">key</span></span><span class="p"><span class="idiff right">)</span>:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="167" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC167" class="line" lang="python">                    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;"><span class="idiff left">key</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">in</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">subs</span></span><span class="p">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python">                        <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+=</span> <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">qv</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python">                    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="170" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="python">                        <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">][</span><span class="n" style="color: #333;">qv</span><span class="p">]</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -174,32 +174,32 @@ def print_subs(subs):</td>

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<td class="diff-line-num old_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">The expected substition frequencies before and after scaling using the scaled qualities as probalities:"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

175

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"C"</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># the special case of no substitutions</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-pvals_before"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"C"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"C"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-pvals_before"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"C"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"C"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

178

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178

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<td class="diff-line-num new_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

179

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">CT</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">NA"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

180

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<td class="diff-line-num new_line" data-linenumber="180" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

180

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"T"</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" 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">

181

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<td class="diff-line-num new_line 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="LC181" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">TC</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"TC-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"T"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"TC-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"T"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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">

181

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<pre style="margin: 0;">+<span id="LC181" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">TC</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"TC-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"T"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"TC-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"T"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

182

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<td class="diff-line-num new_line" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

182

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="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">

183

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<td class="diff-line-num new_line" 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">

183

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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="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">TC</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">NA"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

184

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<td class="diff-line-num new_line" data-linenumber="184" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

184

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"G"</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

185

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<td class="diff-line-num new_line old" data-linenumber="185" style="width: 35px; color: rgba(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 class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-pvals_before"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"G"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"G"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="185" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC185" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-pvals_before"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"G"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"G"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

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186

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186

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<pre style="margin: 0;"> <span id="LC186" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

187

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<td class="diff-line-num new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

187

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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">GA</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">NA"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<td class="diff-line-num new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

188

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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python">    <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"A"</span><span class="p">]</span><span class="o" style="font-weight: 600;">!=</span><span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

189

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<td class="diff-line-num new_line old" data-linenumber="189" style="width: 35px; color: rgba(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="LC189" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">AG</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"AG-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"A"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"AG-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"A"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

189

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<pre style="margin: 0;">+<span id="LC189" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">AG</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"AG-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"A"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"AG-pvals"</span></span><span class="p"><span class="idiff">]</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"A"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="190" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

190

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190

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

191

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<td class="diff-line-num new_line" data-linenumber="191" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">AG</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">NA</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">NA"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<td class="diff-line-num new_line" data-linenumber="192" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

192

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Quality metrics before and after scaling"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

193

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<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC193" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q0 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q0"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q0"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

194

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<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC194" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q10 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q10"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q10"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

195

</td>

<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC195" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q20 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q20"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q20"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

196

</td>

<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC196" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q30 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q30"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q30"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

197

</td>

<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC197" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q40 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q40"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q40"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

198

</td>

<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC198" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q0 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q0"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q0"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

199

</td>

<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC199" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q10 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q10"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q10"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

200

</td>

<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC200" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q20 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q20"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q20"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="201" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

201

</td>

<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC201" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q30 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q30"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q30"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="diff-line-num old old_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

202

</td>

<td class="diff-line-num new_line old" data-linenumber="193" style="width: 35px; color: rgba(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="LC202" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q40 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q40"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q40"</span></span><span class="p"><span class="idiff right">]</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="193" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

193

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC193" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q0 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q0"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q0"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

194

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC194" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q10 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q10"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q10"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="195" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

195

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC195" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q20 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q20"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q20"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

196

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC196" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q30 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q30"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q30"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

197

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC197" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">CT-Q40 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-before-Q40"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"CT-after-Q40"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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">

198

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<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="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q0 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q0"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q0"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="199" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

199

</td>

<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC199" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q10 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q10"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q10"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="200" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC200" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q20 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q20"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q20"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="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">

201

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<pre style="margin: 0;">+<span id="LC201" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q30 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q30"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q30"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="203" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="202" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

202

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<pre style="margin: 0;">+<span id="LC202" 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;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">GA-Q40 </span></span><span class="se" style="color: #d14;"><span class="idiff">\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-before-Q40"</span></span><span class="p"><span class="idiff">])</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="se" style="color: #d14;"><span class="idiff">\t\t</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">subs</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">"GA-after-Q40"</span></span><span class="p"><span class="idiff right">])</span>))</span></span>

</pre>

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<td class="diff-line-num old_line" 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="diff-line-num new_line" 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">

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="python">    </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="204" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="205" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rescale_qual_read</span><span class="p">(</span><span class="n" style="color: #333;">bam</span><span class="p">,</span> <span class="n" style="color: #333;">read</span><span class="p">,</span> <span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">corr_prob</span><span class="p">,</span><span class="n" style="color: #333;">subs</span><span class="p">,</span> <span class="n" style="color: #333;">debug</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;">direction</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"both"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -237,7 +237,7 @@ def rescale_qual_read(bam, read, ref, corr_prob,subs, debug = False,direction="b</td>

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<td class="diff-line-num old_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="237" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="python">    <span class="n" style="color: #333;">new_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">100</span><span class="p">]</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">length_read</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="238" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

238

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python">    <span class="n" style="color: #333;">pos_on_read</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="239" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">    <span class="n" style="color: #333;">number_of_rescaled_bases</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

240

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<td class="diff-line-num new_line old" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">nt_seq</span><span class="p">,</span> <span class="n" style="color: #333;">nt_ref</span><span class="p">,</span> <span class="n" style="color: #333;">nt_qual</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;"><span class="idiff left">itertools</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">izip</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff right">x</span>range</span><span class="p">(</span><span class="n" style="color: #333;">length_align</span><span class="p">),</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">refseq</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="240" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC240" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">i</span><span class="p">,</span> <span class="n" style="color: #333;">nt_seq</span><span class="p">,</span> <span class="n" style="color: #333;">nt_ref</span><span class="p">,</span> <span class="n" style="color: #333;">nt_qual</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">zip</span></span><span class="p"><span class="idiff right">(</span></span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length_align</span><span class="p">),</span> <span class="n" style="color: #333;">seq</span><span class="p">,</span> <span class="n" style="color: #333;">refseq</span><span class="p">,</span> <span class="n" style="color: #333;">qual</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

241

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<td class="diff-line-num new_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># rescale the quality according to the triplet position, </span></span>

</pre>

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242

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># pair of the reference and the sequence</span></span>

</pre>

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243

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="n" style="color: #333;">nt_seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"T"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nt_ref</span> <span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"C"</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">nt_seq</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"A"</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">nt_ref</span> <span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">"G"</span><span class="p">)):</span></span>

</pre>

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<br>

</li>

<li id="75b02a5c976ccbaf5ae0eb096d80048de9e6c6d5">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#75b02a5c976ccbaf5ae0eb096d80048de9e6c6d5"><strong>mapdamage/rescale_test.py</strong></a>

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1

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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;">unittest</span></span>

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2

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2

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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;">optparse</span></span>

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3

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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;">rescale</span></span>

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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;"><span class="idiff left">from</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">.</span></span><span class="idiff right"> </span><span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">rescale</span></span>

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4

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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;">pysam</span></span>

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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;">filecmp</span></span>

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>

</pre>

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</li>

<li id="017dc3d29c7a52f7f3babb6888efcd4925648636">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#017dc3d29c7a52f7f3babb6888efcd4925648636"><strong>mapdamage/rscript.py</strong></a>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"></span>

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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;">os</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;">subprocess</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">subprocess</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">CalledProcessError</span><span class="p">,</span> <span class="n" style="color: #333;">check_call</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,8 +13,8 @@ def construct_path(name,folder="Rscripts"):</td>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">plot</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">  <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;">  Calls the R script to make the plots, takes in the arguments<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"><span class="s" style="color: #d14;">  from parameter processing<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"><span class="s" style="color: #d14;">  Calls the R script to make the plots, takes in the arguments</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="s" style="color: #d14;">  from parameter processing</span></span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="python"><span class="s" style="color: #d14;">  """</span></span>

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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">  <span class="c1" style="color: #998; font-style: italic;"># comp<-args[1]</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python">  <span class="c1" style="color: #998; font-style: italic;"># pdfout<-args[2]</span></span>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -32,33 +30,33 @@ def plot(opt):</td>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">  <span class="n" style="color: #333;">fcomp</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"dnacomp.txt"</span></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">  <span class="n" style="color: #333;">title</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"Fragmisincorporation_plot.pdf"</span></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python">  <span class="n" style="color: #333;">script</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_path</span><span class="p">(</span><span class="s" style="color: #d14;">"mapDamage.R"</span><span class="p">)</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new old_line" 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="LC33" class="line" lang="python">  <span class="n" style="color: #333;">script</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_path</span><span class="p">(</span><span class="s" style="color: #d14;">"mapDamage.R"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">  <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Rscript"</span><span class="p">,</span> <span class="n" style="color: #333;">script</span><span class="p">,</span> <span class="n" style="color: #333;">fcomp</span><span class="p">,</span> <span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">refplot</span><span class="p">,</span> <span class="n" style="color: #333;">fmut</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readplot</span><span class="p">,</span> \</span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">      <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ymax</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">__version__</span><span class="p">]</span></span>

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<td class="diff-line-num old old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python">  <span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">call</span></span><span class="p">))</span></span>

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<td class="diff-line-num new old_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); 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;">code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">call</span></span><span class="p"><span class="idiff right">)</span>))</span></span>

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

37

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

38

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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;">code</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="diff-line-num new_line" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

39

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<pre style="margin: 0;"> <span id="LC39" 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;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

42

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<td class="diff-line-num new_line old" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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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="LC42" class="line" lang="python">      <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"pdf </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s generated"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">title</span></span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="40" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC40" 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;"><span class="idiff">"pdf </span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">s generated"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">title</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<td class="diff-line-num new_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

41

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC41" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

42

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC42" class="line" lang="python">  <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="diff-line-num new_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

43

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: plotting with R failed"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

47

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<td class="diff-line-num new_line" data-linenumber="45" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

45

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

46

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC46" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="47" style="width: 35px; color: rgba(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="LC49" class="line" lang="python"><span class="idiff left right">        </span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="47" style="width: 35px; color: rgba(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="LC50" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">opt_plots</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">):</span><span class="idiff left right">       </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

47

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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="LC47" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">opt_plots</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

51

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<td class="diff-line-num new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

49

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC49" class="line" lang="python">  <span class="s" style="color: #d14;">""" optional plots for length distribution</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

52

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

50

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"><span class="s" style="color: #d14;">  and cumulative C>T mutations, per strand """</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

53

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<td class="diff-line-num new_line old" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="idiff left right">  </span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

51

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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="LC51" class="line" lang="python"></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python">  <span class="n" style="color: #333;">fmut</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"misincorporation.txt"</span></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python">  <span class="n" style="color: #333;">flength</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"lgdistribution.txt"</span></span>

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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python">  <span class="n" style="color: #333;">output</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"Length_plot.pdf"</span></span>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python">  <span class="n" style="color: #333;">script</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_path</span><span class="p">(</span><span class="s" style="color: #d14;">"lengths.R"</span><span class="p">)</span><span class="idiff left right"> </span></span>

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<td class="diff-line-num new old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python">  <span class="n" style="color: #333;">script</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">construct_path</span><span class="p">(</span><span class="s" style="color: #d14;">"lengths.R"</span><span class="p">)</span></span>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python">  <span class="n" style="color: #333;">call</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"Rscript"</span><span class="p">,</span> <span class="n" style="color: #333;">script</span><span class="p">,</span> <span class="n" style="color: #333;">flength</span><span class="p">,</span> <span class="n" style="color: #333;">output</span><span class="p">,</span> <span class="n" style="color: #333;">fmut</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">length</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;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">title</span><span class="p">,</span> <span class="n" style="color: #333;">__version__</span><span class="p">,</span> <span class="n" style="color: #333;">bool_to_int</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">quiet</span><span class="p">)]</span></span>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="python">  <span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">call</span></span><span class="p">))</span></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="python">  <span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">call</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">map</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">call</span></span><span class="p"><span class="idiff right">)</span>))</span></span>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python">  <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">code</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">0</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">0</span></span>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python">  <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="77" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="75" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -77,7 +75,7 @@ def check_R_one_lib(name):</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">check_R_lib</span><span class="p">():</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python">    <span class="s" style="color: #d14;">"""</span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;">    Checks if the necessary R libraries are here, signal<span class="idiff left right"> </span></span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"><span class="s" style="color: #d14;">    Checks if the necessary R libraries are here, signal</span></span>

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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"><span class="s" style="color: #d14;">    otherwise</span></span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"><span class="s" style="color: #d14;">    """</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="python">    <span class="n" style="color: #333;">libs</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="s" style="color: #d14;">"inline"</span><span class="p">,</span> <span class="s" style="color: #d14;">"ggplot2"</span><span class="p">,</span> <span class="s" style="color: #d14;">"gam"</span><span class="p">,</span> <span class="s" style="color: #d14;">"Rcpp"</span><span class="p">,</span> <span class="s" style="color: #d14;">"RcppGSL"</span><span class="p">]</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,11 +88,11 @@ def check_R_lib():</td>

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<pre style="margin: 0;"> <span id="LC88" 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;">missing_lib</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="LC89" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># Grammar Nazi has arrived</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python">        <span class="n" style="color: #333;">last_ele</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">missing_lib</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pop</span><span class="p">()</span></span>

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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="idiff left right"> </span><span class="p">(</span><span class="s" style="color: #d14;">"Missing the following R libraries '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"', '"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">missing_lib</span><span class="p">)</span> \</span>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="python">            <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"' and '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_ele</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"'"</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC91" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p"><span class="idiff left right">(</span>(</span><span class="s" style="color: #d14;">"Missing the following R libraries '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"', '"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">missing_lib</span><span class="p">)</span> \</span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="python">            <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"' and '"</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">last_ele</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"'"</span><span class="p">)<span class="idiff left right">)</span></span></span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="python">    <span class="k" style="font-weight: 600;">elif</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">missing_lib</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="LC97" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="idiff left"> </span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"Missing the following R library "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">missing_lib</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">]</span>)</span></span>

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<pre style="margin: 0;">+<span id="LC95" 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;"><span class="idiff">"Missing the following R library "</span></span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="n" style="color: #333;"><span class="idiff">missing_lib</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">])</span>)</span></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="mi" style="color: #099;">1</span></span>

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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="python">    <span class="k" style="font-weight: 600;">else</span> <span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="100" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="python">        <span class="c1" style="color: #998; font-style: italic;"># No missing libraries</span></span>

</pre>

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<br>

</li>

<li id="f1abf675c9546a833e1e6a8ab63806c189f1d0e5">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#f1abf675c9546a833e1e6a8ab63806c189f1d0e5"><strong>mapdamage/seq.py</strong></a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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2

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<td class="diff-line-num new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="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="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<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;">string</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

5

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<td class="diff-line-num new_line" data-linenumber="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="c1" style="color: #998; font-style: italic;"># from Martin Kircher, to complement DNA</span></span>

</pre>

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<td class="diff-line-num new_line 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="n" style="color: #333;">TABLE</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">str<span class="idiff left right">ing</span></span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maketrans</span><span class="p">(</span><span class="s" style="color: #d14;">'TGCAMRWSYKVHDBtgcamrwsykvhdb'</span><span class="p">,</span> \</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">TABLE</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">str</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">maketrans</span><span class="p">(</span><span class="s" style="color: #d14;">'TGCAMRWSYKVHDBtgcamrwsykvhdb'</span><span class="p">,</span> \</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python">    <span class="s" style="color: #d14;">'ACGTKYWSRMBDHVacgtkywsrmbdhv'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="n" style="color: #333;">LETTERS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">"A"</span><span class="p">,</span> <span class="s" style="color: #d14;">"C"</span><span class="p">,</span> <span class="s" style="color: #d14;">"G"</span><span class="p">,</span> <span class="s" style="color: #d14;">"T"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="n" style="color: #333;">MUTATIONS</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="s" style="color: #d14;">'G>A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C>T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A>G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T>C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A>C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A>T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C>G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C>A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T>G'</span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python">             <span class="s" style="color: #d14;">'T>A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G>C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G>T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A>-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T>-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C>-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G>-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'->A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'->T'</span><span class="p">,</span><span class="idiff left right"> </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="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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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python">             <span class="s" style="color: #d14;">'T>A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G>C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G>T'</span><span class="p">,</span> <span class="s" style="color: #d14;">'A>-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'T>-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'C>-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'G>-'</span><span class="p">,</span> <span class="s" style="color: #d14;">'->A'</span><span class="p">,</span> <span class="s" style="color: #d14;">'->T'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python">             <span class="s" style="color: #d14;">'->C'</span><span class="p">,</span> <span class="s" style="color: #d14;">'->G'</span><span class="p">,</span> <span class="s" style="color: #d14;">'S'</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"><span class="n" style="color: #333;">HEADER</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">LETTERS</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">(</span><span class="s" style="color: #d14;">"Total"</span><span class="p">,</span> <span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">MUTATIONS</span></span>

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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -33,11 +32,11 @@ def record_lg(read, coordinate, tab):</td>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">  <span class="s" style="color: #d14;">""" record global length distribution</span></span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python"><span class="s" style="color: #d14;">  don't record paired reads as they are normally not used for aDNA """</span></span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="python">  <span class="n" style="color: #333;">std</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'-'</span> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_reverse</span> <span class="k" style="font-weight: 600;">else</span> <span class="s" style="color: #d14;">'+'</span></span>

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<td class="diff-line-num new_line 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="LC36" class="line" lang="python"><span class="idiff left right">  </span></span>

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<td class="diff-line-num new old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python">  <span class="n" style="color: #333;">length</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="nb" style="color: #0086b3;">max</span><span class="p">(</span><span class="n" style="color: #333;">coordinate</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nb" style="color: #0086b3;">min</span><span class="p">(</span><span class="n" style="color: #333;">coordinate</span><span class="p">))</span></span>

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<td class="diff-line-num old_line" data-linenumber="38" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" 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;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_paired</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="python">    <span class="n" style="color: #333;">tab</span><span class="p">[</span><span class="n" style="color: #333;">std</span><span class="p">][</span><span class="n" style="color: #333;">length</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tab</span><span class="p">[</span><span class="n" style="color: #333;">std</span><span class="p">][</span><span class="n" style="color: #333;">length</span><span class="p">]</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span></span>

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<td class="diff-line-num new_line old" data-linenumber="39" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="python"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tab</span></span>

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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -47,7 +46,7 @@ def read_fasta_index(filename):</td>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">msg</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python">    <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"       Filename: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">filename</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;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"       Line:     </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="nb" style="color: #0086b3;">repr</span><span class="p">(</span><span class="n" style="color: #333;">line</span><span class="p">))</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"><span class="idiff left right">  </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">  <span class="n" style="color: #333;">fai</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python">  <span class="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;">filename</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;">handle</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="53" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" 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;">handle</span><span class="p">:</span></span>

</pre>

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</table>

<br>

</li>

<li id="e355b413f51f144a95b8d6b33f74ce254bdbbdd2">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#e355b413f51f144a95b8d6b33f74ce254bdbbdd2"><strong>mapdamage/tables.py</strong></a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="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>

</pre>

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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;">os</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">collections</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +5,7 @@ import mapdamage</td>

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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;">mapdamage.version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>

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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">initialize_mut</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">):</span><span class="idiff left right">  </span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">initialize_mut</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python">  <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="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="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref</span><span class="p">:</span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python">    <span class="n" style="color: #333;">tab_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tab</span><span class="p">[</span><span class="n" style="color: #333;">contig</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,8 +14,8 @@ def initialize_mut(ref, length):</td>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python">      <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">std</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span><span class="s" style="color: #d14;">'-'</span><span class="p">):</span></span>

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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="python">        <span class="n" style="color: #333;">tab_std</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">tab_end</span><span class="p">[</span><span class="n" style="color: #333;">std</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<td class="diff-line-num new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">mut</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">HEADER</span><span class="p">:</span></span>

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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python">          <span class="n" style="color: #333;">tab_std</span><span class="p">[</span><span class="n" style="color: #333;">mut</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fromkeys</span><span class="p">(</span><span class="nb" style="color: #0086b3;"><span class="idiff left right">x</span>range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<td class="diff-line-num new_line old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="python"><span class="idiff left right">  </span></span>

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<td class="diff-line-num new old_line" data-linenumber="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="LC17" class="line" lang="python">          <span class="n" style="color: #333;">tab_std</span><span class="p">[</span><span class="n" style="color: #333;">mut</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">fromkeys</span><span class="p">(</span><span class="nb" style="color: #0086b3;">range</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">),</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tab</span></span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,8 +24,8 @@ def print_mut(mut, opt, out):</td>

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<td class="diff-line-num old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">initialize_comp</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">around</span><span class="p">,</span> <span class="n" style="color: #333;">length</span><span class="p">):</span></span>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python">  <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"3p"</span> <span class="p">:</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">range</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">around</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python">          <span class="s" style="color: #d14;">"5p"</span> <span class="p">:</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">range</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">around</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)}</span></span>

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<td class="diff-line-num new new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="python">  <span class="n" style="color: #333;">keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">"3p"</span> <span class="p">:</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">range</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">length</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">around</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>),</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python">          <span class="s" style="color: #d14;">"5p"</span> <span class="p">:</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">range</span></span><span class="p"><span class="idiff">(</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">around</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff">))</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">list</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">range</span></span><span class="p"><span class="idiff">(</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">length</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">+</span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">)</span>)}</span></span>

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python">  <span class="n" style="color: #333;">tab</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">contig</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">ref</span><span class="p">:</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -52,7 +50,7 @@ def initialize_lg():</td>

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">std</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">'+'</span><span class="p">,</span><span class="s" style="color: #d14;">'-'</span><span class="p">):</span></span>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python">    <span class="n" style="color: #333;">tab</span><span class="p">[</span><span class="n" style="color: #333;">std</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">collections</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">defaultdict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">int</span><span class="p">)</span></span>

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<td class="diff-line-num new_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tab</span><span class="idiff left right"> </span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">tab</span></span>

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<td class="diff-line-num new_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"></span>

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<td class="diff-line-num new_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">print_lg</span><span class="p">(</span><span class="n" style="color: #333;">tab</span><span class="p">,</span> <span class="n" style="color: #333;">opt</span><span class="p">,</span> <span class="n" style="color: #333;">out</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="74" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -74,8 +72,8 @@ def check_table_and_warn_if_dmg_freq_is_low(folder):</td>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python">  <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.0</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">filename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"5pCtoT_freq.txt"</span><span class="p">,</span> <span class="s" style="color: #d14;">"3pGtoA_freq.txt"</span><span class="p">):</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC74" 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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">exists</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">+</span><span class="n" style="color: #333;">filename</span><span class="p">):</span></span>

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77

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python">      <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Required table has not been created ('</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'), bayesian computation cannot be performed"</span> \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="python">            <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="python">      <span class="k" style="font-weight: 600;">print</span><span class="p">(<span class="idiff left right">(</span></span><span class="s" style="color: #d14;">"Error: Required table has not been created ('</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'), bayesian computation cannot be performed"</span> \</span>

</pre>

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<td class="diff-line-num new old_line" 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">

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="python">            <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">filename</span><span class="p">)<span class="idiff left right">)</span></span></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python">      <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC79" 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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">))</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="85" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -85,12 +83,12 @@ def check_table_and_warn_if_dmg_freq_is_low(folder):</td>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="python">          <span class="n" style="color: #333;">total</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;">freq</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="LC84" class="line" lang="python">          <span class="k" style="font-weight: 600;">break</span></span>

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<pre style="margin: 0;"> <span id="LC85" 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="LC88" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"Error: Could not find pos = 1 in table '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s', bayesian computation cannot be performed"</span> \</span>

</pre>

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="python">              <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" 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="LC86" class="line" lang="python">        <span class="k" style="font-weight: 600;">print</span><span class="p">(<span class="idiff left right">(</span></span><span class="s" style="color: #d14;">"Error: Could not find pos = 1 in table '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s', bayesian computation cannot be performed"</span> \</span>

</pre>

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<td class="diff-line-num new old_line" 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="LC87" class="line" lang="python">              <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">filename</span><span class="p">)<span class="idiff left right">)</span></span></span>

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<td class="diff-line-num new_line" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

88

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<pre style="margin: 0;"> <span id="LC88" class="line" lang="python">        <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

91

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<td class="diff-line-num new_line" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

89

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

92

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<td class="diff-line-num new_line" data-linenumber="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

90

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="python">  <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">total</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">0.01</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

93

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<td class="diff-line-num new_line old" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="python">    <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left">"Warning: DNA damage levels are too low, the Bayesian computation should not be performed (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">f < 0.01)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">total</span></span><span class="p">)</span></span>

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<td class="diff-line-num new old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC91" 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;"><span class="idiff">"Warning: DNA damage levels are too low, the Bayesian computation should not be performed (</span></span><span class="si" style="color: #d14;"><span class="idiff">%</span></span><span class="s" style="color: #d14;"><span class="idiff">f < 0.01)</span></span><span class="se" style="color: #d14;"><span class="idiff">\n</span></span><span class="s" style="color: #d14;"><span class="idiff">"</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">%</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">total</span></span><span class="p"><span class="idiff right">)</span>)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="93" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="python">  <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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="python"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -103,9 +101,9 @@ def _print_freq_table(table, columns, opt, out, offset = 0):</td>

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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="python">  <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"# Chr: reference from sam/bam header, End: from which termini of DNA sequences, Std: strand of reads</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="102" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC102" class="line" lang="python">  <span class="n" style="color: #333;">out</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"Chr</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">End</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Std</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">Pos</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="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="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">columns</span><span class="p">)))</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="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>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ite<span class="idiff left right">rite</span>ms</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">strands</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">ends</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ite<span class="idiff left right">rite</span>ms</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="python">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">subtable</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">strands</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">ite<span class="idiff left right">rite</span>ms</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="104" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="python">  <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">reference</span><span class="p">,</span> <span class="n" style="color: #333;">ends</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">table</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">end</span><span class="p">,</span> <span class="n" style="color: #333;">strands</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">ends</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC106" class="line" lang="python">      <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">strand</span><span class="p">,</span> <span class="n" style="color: #333;">subtable</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">strands</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">items</span><span class="p">()):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="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="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

107

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="python">        <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"Total"</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="110" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

110

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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">index</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="n" style="color: #333;">columns</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]):</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

111

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<td class="diff-line-num new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="python">          <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"Total"</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sum</span><span class="p">(</span><span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="n" style="color: #333;">letter</span><span class="p">][</span><span class="n" style="color: #333;">index</span><span class="p">]</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">letter</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">mapdamage</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">seq</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">LETTERS</span><span class="p">)</span></span>

</pre>

</td>

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<br>

</li>

<li id="65134f9708e381a1019a789ae57129129e967d80">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#65134f9708e381a1019a789ae57129129e967d80"><strong>mapdamage/version.py</strong></a>

<hr>

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<td class="diff-line-num old old_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python<span class="idiff left right">3</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="python">    <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mapdamage._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

5

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<td class="diff-line-num new_line old" data-linenumber="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="LC5" class="line" lang="python">    <span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.<span class="idiff left right">0.8</span>"</span></span></pre>

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<td class="diff-line-num new old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="python">    <span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.<span class="idiff left right">1.0</span>"</span></span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8e2edce0d507e1297474f25c00cae94258db38d8">

<a href="https://salsa.debian.org/med-team/mapdamage/compare/88621b984ce2d3ffd54b967e6e64c515fbf18fff...43e9ade9065122eb2e25f2be0a1f8f85f4ab1f28#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</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="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python<span class="idiff left right">3</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># -*- coding: utf-8 -*-</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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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;">distutils.core</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ def setup_version():</td>

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<pre style="margin: 0;"> <span id="LC31" 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;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">path</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"mapdamage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_version.py"</span><span class="p">),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python">            <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#!/usr/bin/env python</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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<td class="diff-line-num old_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="python">            <span class="n" style="color: #333;">handle</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"__version__ = </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">r</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">strip</span><span class="p">(),))</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="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="python">    <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CalledProcessError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">)<span class="idiff left right">,</span></span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="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="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">CalledProcessError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">)</span><span class="idiff left"> </span><span class="k" style="font-weight: 600;"><span class="idiff right">as</span></span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python">        <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not determine mapDamage version: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">error</span><span class="p">,))</span></span>

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<td class="diff-line-num old_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"></span>

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<td class="diff-line-num old_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -46,7 +46,7 @@ class compileInstall(DistutilsInstall):</td>

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<td class="diff-line-num old_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="46" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="python">        <span class="n" style="color: #333;">files</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">get_outputs</span><span class="p">()</span></span>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">fi</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">files</span><span class="p">:</span></span>

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<td class="diff-line-num old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">fi</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="s" style="color: #d14;">"seqtk/seqtk"</span><span class="p">):</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python">                <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chmod</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">,</span><span class="mi" style="color: #099;">0755</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="diff-line-num new new_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python">                <span class="n" style="color: #333;">os</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">chmod</span><span class="p">(</span><span class="n" style="color: #333;">fi</span><span class="p">,</span><span class="mo" style="color: #099;">0<span class="idiff left right">o</span>755</span><span class="p">)</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="51" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -55,7 +55,7 @@ class compileInstall(DistutilsInstall):</td>

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<td class="diff-line-num old_line" data-linenumber="55" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="n" style="color: #333;">setup</span><span class="p">(</span></span>

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<td class="diff-line-num old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python">    <span class="n" style="color: #333;">cmdclass</span><span class="o" style="font-weight: 600;">=</span><span class="p">{</span><span class="s" style="color: #d14;">'install'</span><span class="p">:</span> <span class="n" style="color: #333;">compileInstall</span><span class="p">},</span></span>

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<td class="diff-line-num old_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python">    <span class="n" style="color: #333;">name</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'mapdamage'</span><span class="p">,</span></span>

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<td class="diff-line-num old old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="python">    <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.<span class="idiff left right">0.8</span>'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); 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="LC58" class="line" lang="python">    <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'2.<span class="idiff left right">1.0</span>'</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python">    <span class="n" style="color: #333;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Aurélien Ginolhac, Mikkel Schubert, Hákon Jónsson'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python">    <span class="n" style="color: #333;">author_email</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'MSchubert@snm.ku.dk, jonsson.hakon@gmail.com'</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python">    <span class="n" style="color: #333;">packages</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'mapdamage'</span><span class="p">],</span></span>

</pre>

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