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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mapdamage">Debian Med / mapdamage</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/2d75da747584b1166c8a9200b964ea44c346a9ed">2d75da74</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-13T10:54:26Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.0+dfsg</pre>
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<h4>7 changed files:</h4>
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<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#82aa9fdb0ec083028290c33cc909b125b2200ecb">
mapdamage/mp_test.py
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<li class="file-stats">
<a href="#a30b6a3b0ae4d9941d25e49d20f6a1a496380bc4">
mapdamage/rescale.py
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<li class="file-stats">
<a href="#1cac8e8756d8c4d41429e0d32bf347cffc5f1b98">
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+
mapdamage/tests/probs/Stats_out_MCMC_correct_prob.csv
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<a href="#53ac062f52d5f2f5108b19d930b06287375c96a9">
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mapdamage/tests/test.rescaled.correct.sam
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<li class="file-stats">
<a href="#65134f9708e381a1019a789ae57129129e967d80">
mapdamage/version.py
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<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/mapdamage/commit/2d75da747584b1166c8a9200b964ea44c346a9ed#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## mapDamage</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line old" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/mapdamage2/README.html) <span class="p">[</span><span class="nv" style="color: #008080;">![Conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/mapdamage2.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/mapdamage2/files)</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">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/mapdamage2/README.html) <span class="p">[</span><span class="nv" style="color: #008080;">![Conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/mapdamage2.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/mapdamage2/files) !<span class="p">[</span><span class="nv" style="color: #008080;">Conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/mapdamage2/badges/latest_release_date.svg</span><span class="p">)</span> <span class="p">![</span><span class="nv" style="color: #008080;">Conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/mapdamage2/badges/version.svg</span><span class="p">)</span> <span class="p">[</span><span class="ss" style="color: #990073;">![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.</span><span class="p">]</span>(https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">#### `bioconda` installation</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"><span class="p">-</span> python3 version <span class="gs" style="font-weight: 600;">**2.2.0**</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown">conda install -c bioconda mapdamage2=2.2.0</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="markdown"><span class="p">-</span> python3 version <span class="gs" style="font-weight: 600;">**2.2.0**</span> <span class="gs" style="font-weight: 600;">**with**</span> R and 4 mandatory packages for the Bayesian inference:</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown">conda install -c bioconda mapdamage2=2.2.0=pyr36_1</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Important</span></span>
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<pre style="margin: 0;">-<span id="LC8" 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;">`mapDamage`</span> to use half of the data for estimation of the damage parameters, sorry for the inconvenience.</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="markdown"><span class="p">-</span> From version <span class="sb" style="color: #d14;">`2.2.0`</span> the <span class="sb" style="color: #d14;">`master`</span> branch is requiring <span class="gs" style="font-weight: 600;">**python3**</span> as <span class="sb" style="color: #d14;">`python2`</span> is not supported from 2020-01-01.</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="markdown"><span class="p">-</span> 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;">`mapDamage`</span> to use half of the data for estimation of the damage parameters, sorry for the inconvenience.</span>
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9
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>
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10
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Introduction</span></span>
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11
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<pre style="margin: 0;"> <span id="LC27" 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>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" 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 <span class="gs" style="font-weight: 600;">**Python3**</span> and <span class="gs" style="font-weight: 600;">**R**</span>, which tracks and quantifies DNA damage patterns</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">mapDamage2</span><span class="p">](</span><span class="sx" style="color: #d14;">http<span class="idiff left right">s</span>://geogenetics.ku.dk/publications/mapdamage2.0/</span><span class="p">)</span> is a computational framework written in <span class="gs" style="font-weight: 600;">**Python3**</span> and <span class="gs" style="font-weight: 600;">**R**</span>, which tracks and quantifies DNA damage patterns</span>
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14
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="markdown">among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="markdown"><span class="sb" style="color: #d14;">`mapDamage`</span> was 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<span class="idiff left">://geogenetics.ku.dk/</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> by the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Orlando Group </span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">http://geogenetics.ku.dk/research</span>/research_groups/palaeomix_group/</span><span class="p">)</span>.</span>
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<td class="diff-line-num new new_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="markdown"><span class="sb" style="color: #d14;">`mapDamage`</span> was 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<span class="idiff left">s://geogenetics.ku.dk/</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> by the </span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Orlando Group </span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff right">https://geogenetics.ku.dk</span>/research_groups/palaeomix_group/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Citation</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -29,15 +45,30 @@ Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L.</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="markdown">http://bioinformatics.oxfordjournals.org/content/27/15/2153](http://bioinformatics.oxfordjournals.org/content/27/15/2153)</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Test</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Test<span class="idiff left right"> the no-stats part and rescaling</span></span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"><span class="idiff left right">in the package, </span>you can test <span class="sb" style="color: #d14;">`mapDamage`</span> by running:</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="markdown">you can test <span class="sb" style="color: #d14;">`mapDamage`</span> by running:</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown">cd mapDamage/mapdamage/</span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="markdown">python3 mp_test.py</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="markdown">should return</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="markdown">Started with the command: /usr/local/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"> Reading from 'tests/test.bam'</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"> Writing results to 'tests/results/'</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="markdown">pdf tests/results/Fragmisincorporation_plot.pdf generated</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="markdown">additional tests/results/Length_plot.pdf generated</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="markdown">Successful run</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="markdown">.</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="markdown">----------------------------------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="markdown">Ran 2 tests in 3.357s</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="markdown">OK</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Contact</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown">Please report bugs and suggest possible improvements to Aurélien Ginolhac, Mikkel Schubert or Hákon Jónsson by email:</span>
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<a href="https://salsa.debian.org/med-team/mapdamage/commit/2d75da747584b1166c8a9200b964ea44c346a9ed#82aa9fdb0ec083028290c33cc909b125b2200ecb"><strong>mapdamage/mp_test.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">unittest</span></span>
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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;">subprocess</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="python"></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;">pysam</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;">mapdamage</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">optparse</span></span>
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6
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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;">filecmp</span></span>
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4
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"></span>
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5
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8
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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;">read_nocomment</span><span class="p">(</span><span class="n" style="color: #333;">dnacomp</span><span class="p">):</span></span>
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6
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9
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<pre style="margin: 0;"> <span id="LC9" 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;">dnacomp</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;">f</span><span class="p">:</span></span>
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7
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10
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="n" style="color: #333;">a</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">f</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">readlines</span><span class="p">()</span></span>
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8
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">[</span><span class="n" style="color: #333;">x</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">x</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">a</span> <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">x</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;">'#'</span><span class="p">)]</span></span>
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9
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">mock_options</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">,</span><span class="n" style="color: #333;">rescale_out</span><span class="p">,</span><span class="n" style="color: #333;">folder</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="python"> <span class="s" style="color: #d14;">"""Make the options object with nice values for testing"""</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">optparse</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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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="python"> <span class="s" style="color: #d14;">"filename"</span><span class="p">:</span><span class="n" style="color: #333;">filename</span><span class="p">,</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"> <span class="s" style="color: #d14;">"rescale_out"</span><span class="p">:</span><span class="n" style="color: #333;">rescale_out</span><span class="p">,</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="python"> <span class="s" style="color: #d14;">"verbose"</span><span class="p">:</span><span class="bp" style="color: #999;">True</span><span class="p">,</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"folder"</span><span class="p">:</span><span class="n" style="color: #333;">folder</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="python"> <span class="s" style="color: #d14;">"rescale_length_5p"</span><span class="p">:</span><span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># default values as in --seq-length</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"rescale_length_3p"</span><span class="p">:</span><span class="mi" style="color: #099;">12</span><span class="p">,</span> <span class="c1" style="color: #998; font-style: italic;"># default values as in --seq-length</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"> <span class="s" style="color: #d14;">"quiet"</span><span class="p">:</span><span class="bp" style="color: #999;">True</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"> <span class="p">})</span></span>
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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="LC26" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">testCases</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_no_stats</span><span class="p">(</span><span class="bp" style="color: #999;">self</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">@@ -14,5 +30,31 @@ class testCases(unittest.TestCase):</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">subprocess</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">run</span><span class="p">([</span><span class="s" style="color: #d14;">"mapDamage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-i"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tests/test.bam"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-r"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tests/fake1.fasta"</span><span class="p">,</span> <span class="s" style="color: #d14;">"-d"</span><span class="p">,</span> <span class="s" style="color: #d14;">"tests/results"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--no-stats"</span><span class="p">],</span> <span class="n" style="color: #333;">check</span> <span class="o" style="font-weight: 600;">=</span> <span class="bp" style="color: #999;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">read_nocomment</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/dnacomp.txt"</span><span class="p">)</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">read_nocomment</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/results/dnacomp.txt"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">testRescaling</span><span class="p">(</span><span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">TestCase</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_single_end_file</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test, rescaling BAM file"""</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The expected substition frequencies before and after scaling using the scaled qualities as probalities:</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CT 0.06226411977920493 0.04163524443356556</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># TC 0.020395286584806528 0.020395286584806528</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># GA 0.04400459948304954 0.03794905109091021</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># AG 0.05355350777642983 0.05355350777642983</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Quality metrics before and after scaling</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CT-Q0 5 5</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CT-Q10 5 2</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CT-Q20 3 2</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CT-Q30 3 2</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CT-Q40 0 0</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># GA-Q0 5 5</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># GA-Q10 5 4</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># GA-Q20 1 0</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># GA-Q30 1 0</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># GA-Q40 0 0</span></span>
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<pre style="margin: 0;">+<span id="LC53" 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;">mock_options</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/test.bam"</span><span class="p">,</span><span class="s" style="color: #d14;">"tests/test.rescaled.sam"</span><span class="p">,</span><span class="s" style="color: #d14;">"tests/probs/"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC54" 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="s" style="color: #d14;">"tests/fake1.fasta"</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC55" 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;">rescale</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">rescale_qual</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span><span class="n" style="color: #333;">options</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;">True</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">assertTrue</span><span class="p">(</span><span class="n" style="color: #333;">filecmp</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">cmp</span><span class="p">(</span><span class="s" style="color: #d14;">"tests/test.rescaled.sam"</span><span class="p">,</span><span class="s" style="color: #d14;">"tests/test.rescaled.correct.sam"</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span><span class="o" style="font-weight: 600;">==</span><span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"> <span class="n" style="color: #333;">unittest</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">main</span><span class="p">()</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/commit/2d75da747584b1166c8a9200b964ea44c346a9ed#a30b6a3b0ae4d9941d25e49d20f6a1a496380bc4"><strong>mapdamage/rescale.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -19,8 +19,8 @@ def phred_char_to_pval(ch):</td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">get_corr_prob</span><span class="p">(</span><span class="n" style="color: #333;">folder</span><span class="p">,</span> <span class="n" style="color: #333;">rescale_length_5p</span><span class="p">,</span> <span class="n" style="color: #333;">rescale_length_3p</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> Reads the damage probability correction file, returns a<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> dictionary with this structure<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="python"><span class="s" style="color: #d14;"> Reads the damage probability correction file, returns a</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="python"><span class="s" style="color: #d14;"> dictionary with this structure</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="s" style="color: #d14;"> position (one based) - CT - probability</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="s" style="color: #d14;"> - GA - probability</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,21 +28,21 @@ def get_corr_prob(folder, rescale_length_5p, rescale_length_3p):</td>
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<pre style="margin: 0;"> <span id="LC28" 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;">isfile</span><span class="p">(</span><span class="n" style="color: #333;">full_path</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;">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;">"Missing file, the file </span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">Stats_out_MCMC_correct_prob.csv</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">should be in the folder</span><span class="se" style="color: #d14;">\n\t</span><span class="s" style="color: #d14;">"</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="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">Did you run the MCMC estimates of the parameters?"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"> <span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">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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<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>
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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>
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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;">line</span><span class="p">[</span><span class="s" style="color: #d14;">"Position"</span><span class="p">]</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">corr_prob</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;">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>
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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>
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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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<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>
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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 class="c1" style="color: #998; font-style: italic;"># Exclude probabilities for positions outside of user-specified region</span></span>
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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;">list</span><span class="p">(</span><span class="n" style="color: #333;">corr_prob</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()):</span></span>
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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>
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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>
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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;">full_path</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">fi</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC32" 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="n" style="color: #333;">fi</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC33" 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>
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<pre style="margin: 0;">+<span id="LC34" 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>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="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="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">corr_prob</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC36" 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>
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<pre style="margin: 0;">+<span id="LC37" 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>
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<pre style="margin: 0;">+<span id="LC38" 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="LC39" 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>
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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="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">corr_prob</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Exclude probabilities for positions outside of user-specified region</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="n" style="color: #333;">corr_prob</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">()):</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">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>
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<pre style="margin: 0;">+<span id="LC44" 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>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">corr_prob</span></span>
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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="n" style="color: #333;">csv</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Error</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">e</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC47" 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;">'File </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 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="s" style="color: #d14;">"Stats_out_MCMC_correct_prob.csv"</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;">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;">e</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">@@ -50,11 +50,11 @@ def get_corr_prob(folder, rescale_length_5p, rescale_length_3p):</td>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">corr_this_base</span><span class="p">(</span><span class="n" style="color: #333;">corr_prob</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;">pos</span><span class="p">,</span> <span class="n" style="color: #333;">length</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>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> The position specific damaging correction, using the input<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> corr_prob dictionary holding the damage correcting values<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> nt_seq nucleotide in the sequence<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="python"><span class="s" style="color: #d14;"> The position specific damaging correction, using the input</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="python"><span class="s" style="color: #d14;"> corr_prob dictionary holding the damage correcting values</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"><span class="s" style="color: #d14;"> nt_seq nucleotide in the sequence</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="s" style="color: #d14;"> nt_ref nucleotide in the reference</span></span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> pos relative position from the 5' end<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="python"><span class="s" style="color: #d14;"> pos relative position from the 5' end</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"><span class="s" style="color: #d14;"> length length of the sequence</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="python"><span class="s" style="color: #d14;"> direction which end to consider the rescaling</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="s" style="color: #d14;"> returns the correction probability for this particular set</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">@@ -71,8 +71,8 @@ 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="LC71" 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="LC72" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># other transitions/transversions are not affected by damage</span></span>
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<pre style="margin: 0;"> <span id="LC73" 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="LC74" class="line" lang="python"><span class="idiff left right"> </span></span>
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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 class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"></span>
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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>
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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>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">corr_prob</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="90" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -90,7 +90,7 @@ 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="LC90" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"forward"</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;">return</span> <span class="n" style="color: #333;">p5_corr</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">direction</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"backward"</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;">return</span> <span class="n" style="color: #333;">p3_corr</span><span class="idiff left right"> </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="n" style="color: #333;">p3_corr</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="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>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos</span> <span class="o" style="font-weight: 600;"><</span> <span class="nb" style="color: #0086b3;">abs</span><span class="p">(</span><span class="n" style="color: #333;">back_pos</span><span class="p">)</span> <span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># then we use the forward correction</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -151,7 +151,7 @@ def record_subs(subs,nt_seq,nt_ref,nt_qual,nt_newqual,prob_corr):</td>
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<pre style="margin: 0;"> <span id="LC151" 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="LC152" class="line" lang="python"> <span class="n" style="color: #333;">sub_type</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"NN"</span></span>
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<pre style="margin: 0;"> <span id="LC153" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">sub_type</span> <span class="o" style="font-weight: 600;">!=</span> <span class="s" style="color: #d14;">"NN"</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC154" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># record only transitions<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># record only transitions</span></span>
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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python"> <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="n" style="color: #333;">sub_type</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"-before"</span><span class="p">][</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="n" style="color: #333;">nt_qual</span><span class="p">))</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">33</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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156
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"> <span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="n" style="color: #333;">sub_type</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"-after"</span><span class="p">][</span><span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="nb" style="color: #0086b3;">ord</span><span class="p">(</span><span class="n" style="color: #333;">nt_newqual</span><span class="p">))</span><span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">33</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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157
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157
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</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="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>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<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 @@ def print_subs(subs):</td>
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175
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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>
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176
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176
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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>
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177
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177
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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><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;">"</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;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"CT-pvals_before"</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="s" style="color: #d14;">"C"</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"CT-pvals"</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="s" style="color: #d14;">"C"</span><span class="p">])))</span></span>
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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 class="idiff left right"> </span></span>
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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>
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179
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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>
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180
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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>
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181
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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><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;">"</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;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"TC-pvals"</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="s" style="color: #d14;">"T"</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"TC-pvals"</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="s" style="color: #d14;">"T"</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">@@ -200,19 +200,19 @@ def print_subs(subs):</td>
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200
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200
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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><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">GA-Q20 </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"GA-before-Q20"</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"GA-after-Q20"</span><span class="p">])))</span></span>
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201
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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><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">GA-Q30 </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"GA-before-Q30"</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"GA-after-Q30"</span><span class="p">])))</span></span>
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202
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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><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">GA-Q40 </span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"GA-before-Q40"</span><span class="p">])</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">+</span><span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">subs</span><span class="p">[</span><span class="s" style="color: #d14;">"GA-after-Q40"</span><span class="p">])))</span></span>
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203
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<pre style="margin: 0;">-<span id="LC203" class="line" lang="python"><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="python"></span>
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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>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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207
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<pre style="margin: 0;"> <span id="LC207" class="line" lang="python"><span class="s" style="color: #d14;"> bam a pysam bam object</span></span>
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208
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208
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<pre style="margin: 0;"> <span id="LC208" class="line" lang="python"><span class="s" style="color: #d14;"> read a pysam read object</span></span>
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209
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209
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="python"><span class="s" style="color: #d14;"> ref a pysam fasta ref file</span></span>
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210
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<pre style="margin: 0;">-<span id="LC210" class="line" lang="python"><span class="s" style="color: #d14;"> reflengths a dictionary holding the length of the references<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC211" class="line" lang="python"><span class="s" style="color: #d14;"> subs a dictionary holding the corrected number of substition before and after scaling<span class="idiff left right"> </span></span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="python"><span class="s" style="color: #d14;"> reflengths a dictionary holding the length of the references</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="python"><span class="s" style="color: #d14;"> subs a dictionary holding the corrected number of substition before and after scaling</span></span>
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212
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212
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<pre style="margin: 0;"> <span id="LC212" class="line" lang="python"><span class="s" style="color: #d14;"> corr_prob dictionary from get_corr_prob</span></span>
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<pre style="margin: 0;"> <span id="LC213" class="line" lang="python"><span class="s" style="color: #d14;"> returns a read with rescaled quality score</span></span>
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<pre style="margin: 0;">-<span id="LC214" class="line" lang="python"><span class="s" style="color: #d14;"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">-<span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> Iterates through the read and reference, rescales the quality<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="python"><span class="s" style="color: #d14;"> Iterates through the read and reference, rescales the quality</span></span>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="python"><span class="s" style="color: #d14;"> according to corr_prob</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;"> <span id="LC218" 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;">debug</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">@@ -238,7 +238,7 @@ def rescale_qual_read(bam, read, ref, corr_prob,subs, debug = False,direction="b</td>
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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>
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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>
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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;">zip</span><span class="p">(</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>
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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 class="idiff left right"> </span></span></span>
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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>
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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>
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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>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># need to rescale this subs.</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">@@ -250,13 +250,13 @@ def rescale_qual_read(bam, read, ref, corr_prob,subs, debug = False,direction="b</td>
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<pre style="margin: 0;"> <span id="LC250" 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="LC251" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># don't rescale, other bases</span></span>
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">newp</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">phred_char_to_pval</span><span class="p">(</span><span class="n" style="color: #333;">nt_qual</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">newq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nt_qual</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="python"> <span class="n" style="color: #333;">newq</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">nt_qual</span></span>
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">pos_on_read</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length_read</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">new_qual</span><span class="p">[</span><span class="n" style="color: #333;">pos_on_read</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newq</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="python"> <span class="n" style="color: #333;">new_qual</span><span class="p">[</span><span class="n" style="color: #333;">pos_on_read</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">newq</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">record_subs</span><span class="p">(</span><span class="n" style="color: #333;">subs</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="n" style="color: #333;">new_qual</span><span class="p">[</span><span class="n" style="color: #333;">pos_on_read</span><span class="p">],</span><span class="n" style="color: #333;">newp</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">nt_seq</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="LC258" 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;">1</span></span>
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<pre style="margin: 0;">-<span id="LC259" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># done with the aligned portion of the read<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># done with the aligned portion of the read</span></span>
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<pre style="margin: 0;"> <span id="LC260" 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="LC261" 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;">debug</span><span class="p">:</span></span>
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262
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262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning: The aligment of the read is longer than the actual read </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span><span class="p">,(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qname</span><span class="p">))</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -266,7 +266,7 @@ def rescale_qual_read(bam, read, ref, corr_prob,subs, debug = False,direction="b</td>
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266
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266
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">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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267
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267
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="python"> <span class="n" style="color: #333;">new_qual</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">new_qual</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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268
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268
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<pre style="margin: 0;"> <span id="LC268" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">):</span></span>
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269
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<pre style="margin: 0;">-<span id="LC269" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check for soft clipping at forward end<span class="idiff left right"> </span></span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check for soft clipping at forward end</span></span>
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270
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270
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<pre style="margin: 0;"> <span id="LC270" class="line" lang="python"> <span class="n" style="color: #333;">new_qual</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;">qual</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">:</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigar</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">][</span><span class="mi" style="color: #099;">1</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">new_qual</span></span>
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271
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">read</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">cigar</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="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">4</span><span class="p">):</span></span>
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272
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272
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the same backwards</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); 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="285" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -285,7 +285,7 @@ def rescale_qual_read(bam, read, ref, corr_prob,subs, debug = False,direction="b</td>
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285
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="python"></span>
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286
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"></span>
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">rescale_qual</span><span class="p">(</span><span class="n" style="color: #333;">ref</span><span class="p">,</span> <span class="n" style="color: #333;">options</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>
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288
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<pre style="margin: 0;">-<span id="LC288" class="line" lang="python"> <span class="s" style="color: #d14;">"""<span class="idiff left right"> </span></span></span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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289
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289
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<pre style="margin: 0;"> <span id="LC289" class="line" lang="python"><span class="s" style="color: #d14;"> ref a pysam fasta ref file</span></span>
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290
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290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"><span class="s" style="color: #d14;"> bam_filename name of a BAM/SAM file to read</span></span>
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291
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291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"><span class="s" style="color: #d14;"> fi file containing the csv with correction probabilities</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="319" style="width: 35px; color: rgba(0,0,0,0.3); 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">@@ -319,20 +319,20 @@ def rescale_qual(ref, options,debug=False):</td>
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319
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319
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<pre style="margin: 0;"> <span id="LC319" class="line" lang="python"> <span class="k" style="font-weight: 600;">pass</span></span>
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320
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<pre style="margin: 0;"> <span id="LC320" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">hit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qual</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;">debug</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC321" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Cannot rescale base PHRED scores for read '</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s'; no scores assigned."</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">hit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">qname</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">hit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_paired</span> <span class="p">:</span><span class="idiff left right"> </span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="python"> <span class="k" style="font-weight: 600;">elif</span> <span class="n" style="color: #333;">hit</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="LC323" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">first_pair</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;">debug</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC324" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assuming the ends are non-overlapping<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># assuming the ends are non-overlapping</span></span>
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<pre style="margin: 0;"> <span id="LC325" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Warning! Assuming the pairs are non-overlapping, facing inwards and correctly paired."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC326" class="line" lang="python"> <span class="n" style="color: #333;">first_pair</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="LC327" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#5p --------------> 3p</span></span>
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<pre style="margin: 0;"> <span id="LC328" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#3p <-------------- 5p</span></span>
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<pre style="margin: 0;"> <span id="LC329" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pair 1 (inwards)</span></span>
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<pre style="margin: 0;">-<span id="LC330" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#5p ----><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#5p ----></span></span>
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<pre style="margin: 0;"> <span id="LC331" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># <---- 5p</span></span>
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<pre style="margin: 0;"> <span id="LC332" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># A B</span></span>
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<pre style="margin: 0;">-<span id="LC333" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pair 2 (outwards), this happens if the reference is RC this is not supported<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># pair 2 (outwards), this happens if the reference is RC this is not supported</span></span>
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<pre style="margin: 0;"> <span id="LC334" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># ----> 3p</span></span>
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<pre style="margin: 0;">-<span id="LC335" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#3p <----<span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#3p <----</span></span>
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<pre style="margin: 0;"> <span id="LC336" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># A B</span></span>
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<pre style="margin: 0;"> <span id="LC337" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Correct outwards pairs from the 3p and inwards pairs with the 5p end</span></span>
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<pre style="margin: 0;"> <span id="LC338" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="p">((</span><span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">hit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">is_reverse</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">hit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mate_is_reverse</span> <span class="ow" style="font-weight: 600;">and</span> <span class="p">(</span><span class="n" style="color: #333;">hit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pnext</span><span class="o" style="font-weight: 600;">></span><span class="n" style="color: #333;">hit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">pos</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">hit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">tid</span><span class="o" style="font-weight: 600;">==</span><span class="n" style="color: #333;">hit</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">mrnm</span><span class="p">):</span></span>
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<li id="1cac8e8756d8c4d41429e0d32bf347cffc5f1b98">
<a href="https://salsa.debian.org/med-team/mapdamage/commit/2d75da747584b1166c8a9200b964ea44c346a9ed#1cac8e8756d8c4d41429e0d32bf347cffc5f1b98"><strong>mapdamage/tests/probs/Stats_out_MCMC_correct_prob.csv</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">"","Position","C.T","G.A"</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">"1",1,0.653616777018436,0</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">"2",2,0.574821404505089,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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="plaintext">"3",3,0.524660717195785,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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="plaintext">"4",4,0.491676371805506,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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="plaintext">"5",5,0.46919312975022,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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="plaintext">"6",6,0.453361082263795,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">"7",7,0.441882878430246,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<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="plaintext">"8",8,0.433345603590333,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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10
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">"9",9,0.426853067214069,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">"10",10,0.4218187429273,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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12
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">"11",11,0.417847465539491,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
13
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">"12",12,0.414666179579865,0</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">"13",-12,0,0.427459648772127</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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15
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">"14",-11,0,0.430678304009036</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
16
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">"15",-10,0,0.434694598982698</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">"16",-9,0,0.439783285536968</span>
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18
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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="LC18" class="line" lang="plaintext">"17",-8,0,0.446341431282045</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">"18",-7,0,0.454957458647015</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
20
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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="LC20" class="line" lang="plaintext">"19",-6,0,0.466528745659899</span>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
21
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">"20",-5,0,0.482466321045583</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
22
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">"21",-4,0,0.505055143009322</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
23
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">"22",-3,0,0.538101706832429</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">"23",-2,0,0.588153916474448</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">"24",-1,0,0.666277684522864</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/commit/2d75da747584b1166c8a9200b964ea44c346a9ed#53ac062f52d5f2f5108b19d930b06287375c96a9"><strong>mapdamage/tests/test.rescaled.correct.sam</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">@SQ SN:fake1 LN:201</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">@PG ID:bwa PN:bwa VN:0.7.17-r1188 CL:bwa samse -f input.sam fake1.fasta - input.fastq</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">fake1:50-100 0 fake1 69 37 31M * 0 0 CCATGTCGGGCAGGCTGGTCTCGAACTCCTG ////////E6/EE/E/A////E//AAAE/EE XT:A:U NM:i:0 X0:i:1 X1:i:0 XM:i:0 XO:i:0 XG:i:0 MD:Z:31 MR:f:0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">fake1:50-100b 0 fake1 69 37 31M * 0 0 CTATGTCGGGCAGGCTGGTCTCGAACTCCTG /#//////E6/EE/E/A////E//AAAE/EE XT:A:U NM:i:1 X0:i:1 X1:i:0 XM:i:1 XO:i:0 XG:i:0 MD:Z:1C29 MR:f:0.57482</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">fake1:50-100c 4 * 0 0 * * 0 0 CGGTAGAGATGGAGTTTCACCATGTCGGGCAAG //////////////A////////////E6/EE/</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">fake1:50-100d 4 * 0 0 * * 0 0 TAATAGAGATGGAGTTTCACCATGTCGTGCAAG //////////////A////////////E6/EE/</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">fake1:70-120 0 fake1 70 37 38M * 0 0 TATGTCGGGCAGGCTGGTCTCGAACTCCTGACCTCAGA #////6EE//AA6E//E66E/EAEEEEEAEEEAAEEA# XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:0C36G0 MR:f:1.31989</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">fake1:80-130 16 fake1 80 25 41M * 0 0 GAGCTGGTCTCGAACTCCTGACCTCAGGCGATCTGCCTGTC AAABBCCDDFEEEEEAEEEEA/EE/E/AAE//A//E/A/// XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:0A0G37C1 MR:f:0</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">fake1:80-130b 16 fake1 80 25 51M * 0 0 AGGCCGGTCTCGAACTCCTGACCTCAGGCGATCTGCCTGCCTTAACCTCCC AAABBCCDDFEEEEEAEEEEA/EE/E/AAE//A//E/A///E/A$/EE66/ XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:4T37C1G6 MR:f:0.44188</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">fake1:80-130c 16 fake1 80 37 51M * 0 0 AGGCTGGTCTCGAACTCCTGACCTCAGGCGATCTGCCTGCCTTAGCCCCCC AAABBCCDDFEEEEEAEEEEA/EE/E/AAE//A//E/A///E/A//EE66/ XT:A:U NM:i:2 X0:i:1 X1:i:0 XM:i:2 XO:i:0 XG:i:0 MD:Z:42C4T3 MR:f:0</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">fake1:80-130d 16 fake1 80 25 51M * 0 0 AGGCTGGTCTCGAACTCCTGACCTCAGACGATCTGCCTGCCTTAGCCCCCC AAABBCCDDFEEEEEAEEEEA/EE/E/AAE//A//E/A///E/A//EE66/ XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:27G14C4T3 MR:f:0</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/commit/2d75da747584b1166c8a9200b964ea44c346a9ed#65134f9708e381a1019a789ae57129129e967d80"><strong>mapdamage/version.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,4 +2,4 @@</td>
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<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>
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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;">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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<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>
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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">1</span>.0"</span></span></pre>
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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">2</span>.0"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/commit/2d75da747584b1166c8a9200b964ea44c346a9ed#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,8 +4,13 @@</td>
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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>
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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;">distutils.command.install</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">install</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">DistutilsInstall</span></span>
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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;">os</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">subprocess</span></span>
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">version_info</span> <span class="o" style="font-weight: 600;"><</span> <span class="p">(</span><span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;">5</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"At least Python 3.5 is required.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">file</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;">stderr</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="python"> <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="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;">compile_seqtk</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;">"""Compiling the seqtk toolkit"""</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="python"> <span class="n" style="color: #333;">old_wd</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;">getcwd</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">@@ -55,11 +60,11 @@ class compileInstall(DistutilsInstall):</td>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="python"><span class="n" style="color: #333;">setup</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;">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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<pre style="margin: 0;"> <span id="LC62" 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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<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</span>.0'</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;">author</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Aur<span class="idiff left right">élien Ginolhac, Mikkel Schubert, Hákon Jó</span>nsson'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC63" 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">2</span>.0'</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC64" 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;">'Aur<span class="idiff left right">élien Ginolhac, Mikkel Schubert, Ãkon Jó</span>nsson'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC65" 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>
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<pre style="margin: 0;"> <span id="LC66" 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>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">package_data</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 class="p">[</span><span class="s" style="color: #d14;">'Rscripts/*.R'</span><span class="p">,</span><span class="s" style="color: #d14;">'Rscripts/stats/*.R'</span><span class="p">,</span><span class="s" style="color: #d14;">'seqtk/seqtk'</span><span class="p">]},</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">package_data</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 class="p">[</span><span class="s" style="color: #d14;">'Rscripts/*.R'</span><span class="p">,</span><span class="s" style="color: #d14;">'Rscripts/stats/*.R'</span><span class="p">,</span><span class="s" style="color: #d14;">'<span class="idiff left">tests/*'</span></span><span class="p"><span class="idiff">,</span></span><span class="s" style="color: #d14;"><span class="idiff right">'</span>seqtk/seqtk'</span><span class="p">]},</span></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">scripts</span><span class="o" style="font-weight: 600;">=</span><span class="p">[</span><span class="s" style="color: #d14;">'bin/mapDamage'</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">url</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'https://github.com/ginolhac/mapDamage'</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">license</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'LICENSE.txt'</span><span class="p">,</span></span>
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