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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/mapdamage">Debian Med / mapdamage</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/8709d46b6d93aa96afe823c375e1bd6e8313f7fc">8709d46b</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T17:52:19Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/e01d28dc68c20c971e7276f244706607f932ae59">e01d28dc</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T17:52:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.1.1+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/c16ac7becfef4e7c956d3feec10aacc653ac8b9d">c16ac7be</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T17:52:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.1.1+dfsg'
Update to upstream version '2.1.1+dfsg'
with Debian dir 8876efee526631235d79f204b4391cc31b79728d</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/1e1c2a59031c9863b8e104e848a6bf0589b5abdc">1e1c2a59</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T17:52:24Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Standards-Version: 4.4.1
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/e59b987f84b6cf5f6f721dacaf7f8dd638efbce7">e59b987f</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T17:55:15Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">na.rm already added by upstream
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/146b27a77545f11f2c798c1f096b89e665f0dd2d">146b27a7</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T17:58:02Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adjusted patches to new upstream region
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/commit/ac991c66c1eb17abed708778741089fed0ddd3f5">ac991c66</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2019-11-30T18:06:40Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Improved cleanup, rescale_test.py no longer with us
</pre>
</li>
</ul>
<h4>23 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#806a2eb8d45517373c81701d49fefdfd30e648c5">
bin/mapDamage
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">
debian/install
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<li class="file-stats">
<a href="#88645f50aec6faa6b6917074e6c75473dad1acb5">
<span class="deleted-file">
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debian/patches/fix_quantile_na_rm.patch
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<a href="#147455c221c6114d6986278a930dc3b46df0c96c">
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debian/patches/fix_rescale_test.patch
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<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#04da551d7b8b96ce0f039c05c3a01a8f3590d1a0">
debian/patches/use_debian_packaged_seqtk.patch
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<a href="#d97202d39b17c50fc83c976a09e5c652fcdb217c">
mapdamage/Rscripts/stats/function.R
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<a href="#82aa9fdb0ec083028290c33cc909b125b2200ecb">
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mapdamage/mp_test.py
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<a href="#75b02a5c976ccbaf5ae0eb096d80048de9e6c6d5">
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mapdamage/rescale_test.py
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mapdamage/rescale_test/long_align/pe.sam
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mapdamage/rescale_test/long_align/pe_output/Stats_out_MCMC_correct_prob.csv
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mapdamage/rescale_test/long_align/ref.fa
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mapdamage/rescale_test/pe_test/pe.sam
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mapdamage/rescale_test/pe_test/pe_output/Stats_out_MCMC_correct_prob.csv
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mapdamage/rescale_test/pe_test/pe_rescaled_correct.sam
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mapdamage/rescale_test/pe_test/ref.fa
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<a href="#cc6c07ecf59230589550d0f474e10d108b0cd0a4">
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mapdamage/tests/dnacomp.txt
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<a href="#eb01e35f66676b628c6352c0916f2b9979068834">
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mapdamage/tests/fake1.fasta
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<a href="#5b36c51c4f1b27b0dfac8bf20c1832cc35a4786d">
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mapdamage/tests/test.bam
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</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="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>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>
</pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Important</span></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown">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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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Introduction</span></span>
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<pre style="margin: 0;"> <span id="LC11" 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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<td class="diff-line-num new_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">mapDamage2</span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/publications/mapdamage2.0/</span><span class="p">)</span> is a computational framework written in <span class="idiff left right">Python and R</span>, which tracks and quantifies DNA damage patterns</span>
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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;"><span class="idiff left">**Python3**</span></span><span class="idiff"> and </span><span class="gs" style="font-weight: 600;"><span class="idiff right">**R**</span></span>, which tracks and quantifies DNA damage patterns</span>
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<pre style="margin: 0;"> <span id="LC14" 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="LC15" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown"><span class="sb" style="color: #d14;">`mapDamage`</span> is developed at the <span class="p">[</span><span class="nv" style="color: #008080;">Centre for GeoGenetics</span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/</span><span class="p">)</span> by the <span class="p">[</span><span class="nv" style="color: #008080;">Orlando Group </span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/research/research_groups/palaeomix_group/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Web interface</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="markdown">Anna Kostikova from <span class="p">[</span><span class="nv" style="color: #008080;">insideDNA</span><span class="p">](</span><span class="sx" style="color: #d14;">https://insidedna.me</span><span class="p">)</span> implemented a web interface for mapDamage. </span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown">Users can adjust the cloud resources in terms of RAM/CPU to perform their analysis. She wrote a <span class="p">[</span><span class="nv" style="color: #008080;">tutorial</span><span class="p">](</span><span class="sx" style="color: #d14;">https://insidedna.me/tutorials/view/Analysis-ancient-DNA-samples-using-mapDamage</span><span class="p">)</span> explaining how to use this <span class="p">[</span><span class="nv" style="color: #008080;">web interface (sign up required)</span><span class="p">](</span><span class="sx" style="color: #d14;">https://insidedna.me/app#/tools/100648/</span><span class="p">)</span></span>
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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://geogenetics.ku.dk/</span><span class="p">)</span> by the <span class="p">[</span><span class="nv" style="color: #008080;">Orlando Group </span><span class="p">](</span><span class="sx" style="color: #d14;">http://geogenetics.ku.dk/research/research_groups/palaeomix_group/</span><span class="p">)</span>.</span>
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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>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Citation</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">@@ -22,12 +23,21 @@ Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L.</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="ge" style="font-style: italic;">_Bioinformatics_</span> 23rd April 2013. doi: 10.1093/bioinformatics/btt193](http://bioinformatics.oxfordjournals.org/content/early/2013/05/17/bioinformatics.btt193)</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="markdown">The original <span class="idiff left right">mapDamage1 is describ</span>ed in the following article: </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="markdown">The original <span class="sb" style="color: #d14;"><span class="idiff left">`mapDamage1`</span></span><span class="idiff right"> was publish</span>ed in the following article: </span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="markdown">Ginolhac A, Rasmussen M, Gilbert MT, Willerslev E, Orlando L.</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"><span class="err" style="color: #a61717; background-color: #e3d2d2;">[</span>mapDamage: testing for damage patterns in ancient DNA sequences. _Bioinformatics_ 2011 <span class="gs" style="font-weight: 600;">**27**</span>(15):2153-5</span>
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<pre style="margin: 0;"> <span id="LC29" 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="LC30" class="line" lang="markdown"></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="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="LC33" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="markdown">in the package, you can test <span class="sb" style="color: #d14;">`mapDamage`</span> by running:</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="markdown">cd mapDamage/mapdamage/</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="markdown">python3 mp_test.py</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC42" 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="LC43" 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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<br>
</li>
<li id="806a2eb8d45517373c81701d49fefdfd30e648c5">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#806a2eb8d45517373c81701d49fefdfd30e648c5"><strong>bin/mapDamage</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -139,6 +139,20 @@ def _check_mm_option():</td>
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139
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<pre style="margin: 0;"> <span id="LC139" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"The --mapdamage-modules path (path=</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s) must contain the mapdamage module"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">path_to_mm</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">path_to_mm</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">is_paired</span><span class="p">(</span><span class="n" style="color: #333;">alignfile</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="python"> <span class="s" style="color: #d14;">"""</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="python"><span class="s" style="color: #d14;"> check if an alignment file contains paired end data by</span></span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python"><span class="s" style="color: #d14;"> looking at the first 100 reads</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python"></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">read</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">alignfile</span><span class="p">:</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" 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_paired</span><span class="p">:</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">True</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python"> <span class="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">1</span></span>
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153
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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="n" style="color: #333;">n</span> <span class="o" style="font-weight: 600;">==</span> <span class="mi" style="color: #099;">100</span><span class="p">:</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="bp" style="color: #999;">False</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="python"></span>
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156
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="python"></span>
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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;">def</span> <span class="nf" style="color: #900; font-weight: 600;">main</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="python"> <span class="n" style="color: #333;">start_time</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">time</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">@@ -227,6 +241,13 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC241" 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="LC242" class="line" lang="python"> <span class="n" style="color: #333;">in_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python"></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;"># exit SAM/BAM is paired (look at top 100 reads)</span></span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">is_paired</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC246" 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;">error</span><span class="p">(</span><span class="s" style="color: #d14;">"alignment file must be single-ended"</span><span class="p">)</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">stderr</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"alignment file must be single-ended</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="python"> <span class="n" style="color: #333;">sys</span><span class="o" style="font-weight: 600;">.</span><span class="nb" style="color: #0086b3;">exit</span><span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">)</span></span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># reset SAM/BAM to the begining</span></span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="python"> <span class="n" style="color: #333;">in_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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230
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251
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<pre style="margin: 0;"> <span id="LC251" class="line" lang="python"></span>
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231
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252
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<pre style="margin: 0;"> <span id="LC252" class="line" lang="python"> <span class="n" style="color: #333;">reflengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">dict</span><span class="p">(</span><span class="nb" style="color: #0086b3;">list</span><span class="p">(</span><span class="nb" style="color: #0086b3;">zip</span><span class="p">(</span><span class="n" style="color: #333;">in_bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">in_bam</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">lengths</span><span class="p">)))</span></span>
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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># check if references in SAM/BAM are the same in the fasta reference file</span></span>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">mapdamage (2.1.1+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> * New upstream version </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> - eliminates two patches</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> + na.rm </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> + import</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> - rescale_test.py no longer available - simpler build process</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * Standards-Version: 4.4.1</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Sat, 30 Nov 2019 18:52:19 +0100</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">mapdamage (2.1.0+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> * New upstream version</span>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,7 +8,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-setuptools,</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> python3-pysam <!nocheck></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">0</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">Standards-Version: 4.4.<span class="idiff left right">1</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/mapdamage</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/mapdamage.git</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Homepage: https://ginolhac.github.io/mapDamage/</span>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">mapdamage/rescale_test usr/share/doc/mapdamage/tests</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#No longer available?</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#mapdamage/rescale_test usr/share/doc/mapdamage/tests</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#88645f50aec6faa6b6917074e6c75473dad1acb5"><strong>debian/patches/fix_quantile_na_rm.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Nadiya Sitdykova</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Description: change calcSampleStats such as any NA and Nan's are </span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"> removed before quantiles are computed</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2017-03-28</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">Bug: https://github.com/ginolhac/mapDamage/issues/18</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff">--- a/mapdamage/Rscripts/stats/function.R</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/Rscripts/stats/function.R</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="p">@@ -595,8 +595,8 @@</span> calcSampleStats <- function(da,X){</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> pos=da[,"Pos"],</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> mea=apply(X,1,mean),</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> med=apply(X,1,median),</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- loCI=apply(X,1,quantile,c(0.025)),</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- hiCI=apply(X,1,quantile,c(0.975))</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ loCI=apply(X,1,quantile,c(0.025),na.rm=TRUE),</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ hiCI=apply(X,1,quantile,c(0.975),na.rm=TRUE)</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> ))</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#147455c221c6114d6986278a930dc3b46df0c96c"><strong>debian/patches/fix_rescale_test.patch</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Tue, 01 Oct 2019 17:13:12 +0200</span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix import statement in rescale_test.py</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff">--- a/mapdamage/rescale_test.py</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/rescale_test.py</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="p">@@ -1,6 +1,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> import unittest</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> import optparse</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-from . import rescale</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+from mapdamage import rescale</span></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> import pysam</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> import filecmp</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> </span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">use_debian_packaged_seqtk.patch</span></pre>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">fix_quantile_na_rm.patch</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">fix_rescale_test.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#04da551d7b8b96ce0f039c05c3a01a8f3590d1a0"><strong>debian/patches/use_debian_packaged_seqtk.patch</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">@@ -3,8 +3,10 @@ Last-Update: Thu, 28 Jul 2016 15:13:14 +0200</td>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="p">Bug-Debian: https://bugs.debian.org/859090</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="p">Description: Use Debian packaged seqtk</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/setup.py</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Index: mapdamage/setup.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mapdamage.orig/setup.py</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mapdamage/setup.py</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"><span class="p">@@ -6,21 +6,6 @@</span> from distutils.command.install import in</span>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> import os</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> import subprocess</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">@@ -54,9 +56,11 @@ Description: Use Debian packaged seqtk</td>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> scripts=['bin/mapDamage'],</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> url='https://github.com/ginolhac/mapDamage',</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> license='LICENSE.txt',</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/bin/mapDamage</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/bin/mapDamage</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="p">@@ -149,7 +149,7 @@</span> def main():</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mapdamage/bin/mapDamage</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mapdamage.orig/bin/mapDamage</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mapdamage/bin/mapDamage</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -163,7 +163,7 @@</span> def main():</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> sys.path.insert(0,path_to_mm)</span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> import mapdamage</span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> </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">@@ -65,8 +69,10 @@ Description: Use Debian packaged seqtk</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> if not (os.path.isfile(fpath_seqtk) and os.access(fpath_seqtk, os.X_OK)):</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> sys.stderr.write("Seqtk executable not accessible; mapDamage has not\n"</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> "been intalled properly or current user does not\n"</span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/mapdamage/composition.py</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/mapdamage/composition.py</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gh" style="color: #999;">Index: mapdamage/mapdamage/composition.py</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- mapdamage.orig/mapdamage/composition.py</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ mapdamage/mapdamage/composition.py</span></span>
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70
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76
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="diff"><span class="p">@@ -33,7 +33,7 @@</span> def get_base_comp(filename,destination=F</span>
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71
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> Gets the basecomposition of all the sequences in filename</span>
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72
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> and returns the value to destination if given.</span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -13,10 +13,15 @@ override_dh_fixperms:</td>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> find debian -name checkLibraries.R -exec chmod +x \{\} \;</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> find debian -name runGeneral.R -exec chmod +x \{\} \;</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">override_dh_install:</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> dh_install</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> mv `find debian -name rescale_test.py` $(TESTDIR)</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> sed -i 's/^import rescale/from mapdamage &/' $(TESTDIR)/rescale_test.py</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"># rescale_test.py seems to have left the building</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">#override_dh_install:</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"># dh_install</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"># mv `find debian -name rescale_test.py` $(TESTDIR)</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"># sed -i 's/^import rescale/from mapdamage &/' $(TESTDIR)/rescale_test.py</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">override_dh_python3:</span>
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22
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> dh_python3 --no-ext-rename</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> rm -f mapdamage/_version.py</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#d97202d39b17c50fc83c976a09e5c652fcdb217c"><strong>mapdamage/Rscripts/stats/function.R</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">@@ -595,8 +595,8 @@ calcSampleStats <- function(da,X){</td>
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<pre style="margin: 0;"> <span id="LC595" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">pos</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">da</span><span class="p">[,</span><span class="s2" style="color: #d14;">"Pos"</span><span class="p">],</span></span>
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<pre style="margin: 0;"> <span id="LC596" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">mea</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">mean</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC597" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">med</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">median</span><span class="p">),</span></span>
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<pre style="margin: 0;">-<span id="LC598" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">loCI</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">quantile</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">0.025</span><span class="p">)),</span></span>
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<pre style="margin: 0;">-<span id="LC599" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">hiCI</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">quantile</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">0.975</span><span class="p">))</span></span>
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">loCI</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">quantile</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">0.025</span><span class="p">)<span class="idiff left">,</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff">na.rm</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="kc" style="font-weight: 600;"><span class="idiff right">TRUE</span></span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="n" style="color: #333;">hiCI</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">apply</span><span class="p">(</span><span class="n" style="color: #333;">X</span><span class="p">,</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="n" style="color: #333;">quantile</span><span class="p">,</span><span class="nf" style="color: #900; font-weight: 600;">c</span><span class="p">(</span><span class="m" style="color: #099;">0.975</span><span class="p">)<span class="idiff left">,</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="n" style="color: #333;"><span class="idiff">na.rm</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="w" style="color: #bbb;"><span class="idiff"> </span></span><span class="kc" style="font-weight: 600;"><span class="idiff right">TRUE</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC600" class="line" lang="r"><span class="w" style="color: #bbb;"> </span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC601" class="line" lang="r"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC602" class="line" lang="r"></span>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#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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<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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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC5" 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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<pre style="margin: 0;">+<span id="LC6" 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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<pre style="margin: 0;">+<span id="LC7" 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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<pre style="margin: 0;">+<span id="LC8" 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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<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;">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="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC12" 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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<pre style="margin: 0;">+<span id="LC13" class="line" lang="python"> <span class="s" style="color: #d14;">"""regular mapDamage"""</span></span>
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<pre style="margin: 0;">+<span id="LC14" 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="LC15" 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="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="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="LC18" 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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<li id="75b02a5c976ccbaf5ae0eb096d80048de9e6c6d5">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#75b02a5c976ccbaf5ae0eb096d80048de9e6c6d5"><strong>mapdamage/rescale_test.py</strong>
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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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<pre style="margin: 0;">-<span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">optparse</span></span>
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<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;">.</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">rescale</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">pysam</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">filecmp</span></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC7" 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="LC8" 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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<pre style="margin: 0;">-<span id="LC9" 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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10
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<pre style="margin: 0;">-<span id="LC10" 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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<pre style="margin: 0;">-<span id="LC11" 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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<pre style="margin: 0;">-<span id="LC12" 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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<pre style="margin: 0;">-<span id="LC13" 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="LC14" 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="LC15" class="line" lang="python"> <span class="p">})</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">testPairedFile</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="LC19" class="line" lang="python"> <span class="s" style="color: #d14;">"""Tests if rescaling of a paired end file"""</span></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;">test_paired_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="LC21" class="line" lang="python"> <span class="s" style="color: #d14;">"""Test, paired end SAM file"""</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># here is the example</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># >ref</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 5p CGA AAA CGA 3p</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># 3p GCT TTT GCT 5p</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># >r001/1</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># CGA</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># >r001/2</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># GCA</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># The sam file looks like this</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#@HD VN:1.5 SO:coordinate</span></span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#@SQ SN:ref LN:9</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#r001 163 ref 1 30 3M = 7 9 CGA III MR:f:0 #the normal ones</span></span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#r001 83 ref 7 30 3M = 1 -9 TCG III MR:f:0</span></span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#r002 163 ref 1 30 3M = 7 9 TGA III MR:f:0.9 #With one dam subs</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;">#r002 83 ref 7 30 3M = 1 -9 CAA III MR:f:0.009</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;">#r003 83 ref 1 30 3M = 7 9 TGA III #The reverse complement, should not rescale (thus no flags)</span></span>
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#r003 163 ref 7 30 3M = 1 -9 CAA III</span></span>
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<pre style="margin: 0;">-<span id="LC39" 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="LC40" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#hand calculated the correct rescaled sam file in pe_rescaled_correct.sam</span></span>
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<pre style="margin: 0;">-<span id="LC41" 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;">"rescale_test/pe_test/pe.sam"</span><span class="p">,</span><span class="s" style="color: #d14;">"rescale_test/pe_test/pe_rescaled.sam"</span><span class="p">,</span><span class="s" style="color: #d14;">"rescale_test/pe_test/pe_output/"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC42" 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;">"rescale_test/pe_test/ref.fa"</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;">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="LC44" 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;">"rescale_test/pe_test/pe_rescaled.sam"</span><span class="p">,</span><span class="s" style="color: #d14;">"rescale_test/pe_test/pe_rescaled_correct.sam"</span><span class="p">))</span></span>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"><span class="k" style="font-weight: 600;">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="LC47" class="line" lang="python"> <span class="s" style="color: #d14;">"""Various cases that failed"""</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">test_longalignshortread</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="LC49" class="line" lang="python"> <span class="s" style="color: #d14;">"""Check if fails on an aligment longer than the read"""</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"rescale_test/long_align/"</span></span>
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<pre style="margin: 0;">-<span id="LC51" 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="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"pe.sam"</span><span class="p">,</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"pe_out.sam"</span><span class="p">,</span><span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">+</span><span class="s" style="color: #d14;">"pe_output/"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC52" 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;">"rescale_test/pe_test/ref.fa"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="python"> <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="LC54" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;">#Should run without an error</span></span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="python"><span class="k" style="font-weight: 600;">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="LC57" 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/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#51e4fb99dfb6587ee99f54afe5cfb909625de4e1"><strong>mapdamage/rescale_test/long_align/pe.sam</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@HD VN:1.5 SO:coordinate</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">@SQ SN:ref LN:9</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">r001 163 ref 1 30 3M2D = 7 9 CGA III</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#c86d4dd09701948777d8ad8f60c0be134e00d9ed"><strong>mapdamage/rescale_test/long_align/pe_output/Stats_out_MCMC_correct_prob.csv</strong>
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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",1,0.9,0</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">"2",2,0.009,0</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">"3",-2,0,0.09</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">"4",-1,0,0.9</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#bd9470ef4fec2b4bee4657442ebcad502c1a1b9e"><strong>mapdamage/rescale_test/long_align/ref.fa</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">>ref</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">CGAAAACGA</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#4463008a91edf5a371d32c944106a242fb6598f7"><strong>mapdamage/rescale_test/pe_test/pe.sam</strong>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@HD VN:1.5 SO:coordinate</span>
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2
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">@SQ SN:ref LN:9</span>
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3
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">r001 163 ref 1 30 3M = 7 9 CGA III</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">r001 83 ref 7 30 3M = 1 -9 CGA III</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">r002 163 ref 1 30 3M = 7 9 TGA III</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">r002 83 ref 7 30 3M = 1 -9 CAA III</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">r003 83 ref 1 30 3M = 7 9 TGA III</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">r003 163 ref 7 30 3M = 1 -9 CAA III</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#8cf85d6d13b53a87090a09b66815d4ee24689009"><strong>mapdamage/rescale_test/pe_test/pe_output/Stats_out_MCMC_correct_prob.csv</strong>
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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",1,0.9,0</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">"2",2,0.009,0</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">"3",-2,0,0.09</span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">"4",-1,0,0.9</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#e0aa3292207ff2151d4d03b8712f4c8606077c97"><strong>mapdamage/rescale_test/pe_test/pe_rescaled_correct.sam</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">@HD VN:1.5 SO:coordinate</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">@SQ SN:ref LN:9</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">r001 163 ref 1 30 3M = 7 9 CGA III MR:f:0</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">r001 83 ref 7 30 3M = 1 -9 CGA III MR:f:0</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">r002 163 ref 1 30 3M = 7 9 TGA !II MR:f:0.9</span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">r002 83 ref 7 30 3M = 1 -9 CAA I5I MR:f:0.009</span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">r003 83 ref 1 30 3M = 7 9 TGA III</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">r003 163 ref 7 30 3M = 1 -9 CAA III</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#1e3f397938721b505be611478e3814ba4a67483e"><strong>mapdamage/rescale_test/pe_test/ref.fa</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">>ref</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">CGAAAACGA</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#cc6c07ecf59230589550d0f474e10d108b0cd0a4"><strong>mapdamage/tests/dnacomp.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># table produced by mapDamage version b'2.1.0-dirty'</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># using mapped file input.sam and fake1.fasta as reference file</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># Chr: reference from sam/bam header, End: from which termini of DNA sequences, Std: strand of reads</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Chr End Std Pos A C G T Total</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">fake1 3p + -70 0 0 0 0 0</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">fake1 3p + -69 0 0 0 0 0</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">fake1 3p + -68 0 0 0 0 0</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">fake1 3p + -67 0 0 0 0 0</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">fake1 3p + -66 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">fake1 3p + -65 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">fake1 3p + -64 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">fake1 3p + -63 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">fake1 3p + -62 0 0 0 0 0</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">fake1 3p + -61 0 0 0 0 0</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">fake1 3p + -60 0 0 0 0 0</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">fake1 3p + -59 0 0 0 0 0</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">fake1 3p + -58 0 0 0 0 0</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">fake1 3p + -57 0 0 0 0 0</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">fake1 3p + -56 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">fake1 3p + -55 0 0 0 0 0</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">fake1 3p + -54 0 0 0 0 0</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">fake1 3p + -53 0 0 0 0 0</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">fake1 3p + -52 0 0 0 0 0</span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">fake1 3p + -51 0 0 0 0 0</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">fake1 3p + -50 0 0 0 0 0</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">fake1 3p + -49 0 0 0 0 0</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">fake1 3p + -48 0 0 0 0 0</span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">fake1 3p + -47 0 0 0 0 0</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">fake1 3p + -46 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">fake1 3p + -45 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">fake1 3p + -44 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">fake1 3p + -43 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">fake1 3p + -42 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">fake1 3p + -41 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">fake1 3p + -40 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">fake1 3p + -39 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">fake1 3p + -38 0 0 0 1 1</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">fake1 3p + -37 1 0 0 0 1</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">fake1 3p + -36 0 0 0 1 1</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">fake1 3p + -35 0 0 1 0 1</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">fake1 3p + -34 0 0 0 1 1</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">fake1 3p + -33 0 1 0 0 1</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">fake1 3p + -32 0 0 1 0 1</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">fake1 3p + -31 0 2 1 0 3</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">fake1 3p + -30 0 1 1 1 3</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">fake1 3p + -29 2 1 0 0 3</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">fake1 3p + -28 1 0 0 2 3</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">fake1 3p + -27 0 0 3 0 3</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">fake1 3p + -26 0 0 1 2 3</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">fake1 3p + -25 0 3 0 0 3</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">fake1 3p + -24 0 0 2 1 3</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">fake1 3p + -23 0 0 3 0 3</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">fake1 3p + -22 0 0 3 0 3</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">fake1 3p + -21 0 2 0 1 3</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">fake1 3p + -20 2 1 0 0 3</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">fake1 3p + -19 0 0 2 1 3</span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">fake1 3p + -18 0 1 2 0 3</span>
</pre>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">fake1 3p + -17 0 2 1 0 3</span>
</pre>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">fake1 3p + -16 1 0 0 2 3</span>
</pre>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">fake1 3p + -15 1 0 2 0 3</span>
</pre>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">fake1 3p + -14 0 1 2 0 3</span>
</pre>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">fake1 3p + -13 0 0 0 3 3</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">fake1 3p + -12 0 3 0 0 3</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">fake1 3p + -11 0 1 0 2 3</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">fake1 3p + -10 0 2 0 1 3</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">fake1 3p + -9 0 0 3 0 3</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">fake1 3p + -8 3 0 0 0 3</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">fake1 3p + -7 2 1 0 0 3</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">fake1 3p + -6 0 3 0 0 3</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">fake1 3p + -5 0 0 0 3 3</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">fake1 3p + -4 0 3 0 0 3</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">fake1 3p + -3 1 2 0 0 3</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">fake1 3p + -2 0 0 1 2 3</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">fake1 3p + -1 1 0 2 0 3</span>
</pre>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">fake1 3p + 1 2 1 0 0 3</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">fake1 3p + 2 0 2 1 0 3</span>
</pre>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">fake1 3p + 3 1 2 0 0 3</span>
</pre>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">fake1 3p + 4 0 0 0 3 3</span>
</pre>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">fake1 3p + 5 0 3 0 0 3</span>
</pre>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">fake1 3p + 6 2 0 0 1 3</span>
</pre>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">fake1 3p + 7 0 0 3 0 3</span>
</pre>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">fake1 3p + 8 0 1 2 0 3</span>
</pre>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">fake1 3p + 9 0 3 0 0 3</span>
</pre>
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84
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">fake1 3p + 10 0 0 2 1 3</span>
</pre>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">fake1 3p - -70 0 0 0 0 0</span>
</pre>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">fake1 3p - -69 0 0 0 0 0</span>
</pre>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">fake1 3p - -68 0 0 0 0 0</span>
</pre>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">fake1 3p - -67 0 0 0 0 0</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">fake1 3p - -66 0 0 0 0 0</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">fake1 3p - -65 0 0 0 0 0</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">fake1 3p - -64 0 0 0 0 0</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">fake1 3p - -63 0 0 0 0 0</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">fake1 3p - -62 0 0 0 0 0</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">fake1 3p - -61 0 0 0 0 0</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">fake1 3p - -60 0 0 0 0 0</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">fake1 3p - -59 0 0 0 0 0</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">fake1 3p - -58 0 0 0 0 0</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">fake1 3p - -57 0 0 0 0 0</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">fake1 3p - -56 0 0 0 0 0</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">fake1 3p - -55 0 0 0 0 0</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">fake1 3p - -54 0 0 0 0 0</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">fake1 3p - -53 0 0 0 0 0</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">fake1 3p - -52 0 0 0 0 0</span>
</pre>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">fake1 3p - -51 0 0 3 0 3</span>
</pre>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">fake1 3p - -50 0 0 3 0 3</span>
</pre>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">fake1 3p - -49 0 0 3 0 3</span>
</pre>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">fake1 3p - -48 1 0 2 0 3</span>
</pre>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">fake1 3p - -47 0 0 3 0 3</span>
</pre>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">fake1 3p - -46 0 0 3 0 3</span>
</pre>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">fake1 3p - -45 0 2 0 1 3</span>
</pre>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">fake1 3p - -44 0 0 0 3 3</span>
</pre>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">fake1 3p - -43 3 0 0 0 3</span>
</pre>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">fake1 3p - -42 3 0 0 0 3</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">fake1 3p - -41 0 0 4 0 4</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">fake1 3p - -40 1 0 3 0 4</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">fake1 3p - -39 0 4 0 0 4</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">fake1 3p - -38 4 0 0 0 4</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">fake1 3p - -37 0 0 4 0 4</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">fake1 3p - -36 0 0 4 0 4</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">fake1 3p - -35 0 4 0 0 4</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">fake1 3p - -34 4 0 0 0 4</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">fake1 3p - -33 0 0 4 0 4</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">fake1 3p - -32 4 0 0 0 4</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">fake1 3p - -31 0 0 0 4 4</span>
</pre>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">fake1 3p - -30 0 4 0 0 4</span>
</pre>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">fake1 3p - -29 0 0 4 0 4</span>
</pre>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">fake1 3p - -28 0 3 0 1 4</span>
</pre>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">fake1 3p - -27 0 4 0 0 4</span>
</pre>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">fake1 3p - -26 0 0 0 4 4</span>
</pre>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">fake1 3p - -25 0 0 4 0 4</span>
</pre>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">fake1 3p - -24 4 0 0 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="132" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">fake1 3p - -23 0 0 4 0 4</span>
</pre>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">fake1 3p - -22 0 0 4 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">fake1 3p - -21 0 0 0 4 4</span>
</pre>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">fake1 3p - -20 0 4 0 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="136" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">fake1 3p - -19 4 0 0 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="137" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">fake1 3p - -18 0 0 4 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="138" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">fake1 3p - -17 0 0 4 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="139" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">fake1 3p - -16 4 0 0 0 4</span>
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<td class="diff-line-num new new_line" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">fake1 3p - -15 0 0 4 0 4</span>
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<td class="diff-line-num new new_line" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">fake1 3p - -14 0 0 0 4 4</span>
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<td class="diff-line-num new new_line" data-linenumber="142" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">fake1 3p - -13 0 0 0 4 4</span>
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<td class="diff-line-num new new_line" data-linenumber="143" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">fake1 3p - -12 0 4 0 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="144" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
144
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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="LC144" class="line" lang="plaintext">fake1 3p - -11 0 0 4 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
145
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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="LC145" class="line" lang="plaintext">fake1 3p - -10 4 0 0 0 4</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="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
146
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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="LC146" class="line" lang="plaintext">fake1 3p - -9 0 0 4 0 4</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="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
147
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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="LC147" class="line" lang="plaintext">fake1 3p - -8 4 0 0 0 4</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="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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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="LC148" class="line" lang="plaintext">fake1 3p - -7 0 4 0 0 4</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="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
149
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">fake1 3p - -6 0 4 0 0 4</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="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
150
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">fake1 3p - -5 3 0 1 0 4</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="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
151
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">fake1 3p - -4 0 0 4 0 4</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="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
152
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">fake1 3p - -3 0 4 0 0 4</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="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
153
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">fake1 3p - -2 0 3 0 1 4</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="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
154
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">fake1 3p - -1 0 1 0 3 4</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="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
155
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">fake1 3p - 1 0 0 4 0 4</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="156" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
156
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">fake1 3p - 2 0 4 0 0 4</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="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
157
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">fake1 3p - 3 0 4 0 0 4</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="158" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
158
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">fake1 3p - 4 0 4 0 0 4</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">
</td>
<td class="diff-line-num new new_line" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
159
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">fake1 3p - 5 0 0 4 0 4</span>
</pre>
</td>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="160" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
160
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">fake1 3p - 6 4 0 0 0 4</span>
</pre>
</td>
</tr>
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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="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
161
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">fake1 3p - 7 0 4 0 0 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="162" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
162
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">fake1 3p - 8 4 0 0 0 4</span>
</pre>
</td>
</tr>
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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="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
163
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">fake1 3p - 9 0 0 0 4 4</span>
</pre>
</td>
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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="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">fake1 3p - 10 0 0 4 0 4</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">fake1 5p + -10 0 0 1 2 3</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">fake1 5p + -9 0 0 3 0 3</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">fake1 5p + -8 1 0 2 0 3</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">fake1 5p + -7 2 0 1 0 3</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">fake1 5p + -6 0 0 2 1 3</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">fake1 5p + -5 0 0 0 3 3</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">fake1 5p + -4 0 0 0 3 3</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">fake1 5p + -3 0 1 0 2 3</span>
</pre>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">fake1 5p + -2 1 2 0 0 3</span>
</pre>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">fake1 5p + -1 2 1 0 0 3</span>
</pre>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">fake1 5p + 1 0 2 0 1 3</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">fake1 5p + 2 1 1 0 1 3</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">fake1 5p + 3 2 0 0 1 3</span>
</pre>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">fake1 5p + 4 0 0 1 2 3</span>
</pre>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">fake1 5p + 5 0 0 2 1 3</span>
</pre>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">fake1 5p + 6 0 1 0 2 3</span>
</pre>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">fake1 5p + 7 0 2 1 0 3</span>
</pre>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">fake1 5p + 8 0 0 3 0 3</span>
</pre>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">fake1 5p + 9 0 0 3 0 3</span>
</pre>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">fake1 5p + 10 0 1 2 0 3</span>
</pre>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">fake1 5p + 11 1 2 0 0 3</span>
</pre>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">fake1 5p + 12 2 0 1 0 3</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="187" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">fake1 5p + 13 0 0 3 0 3</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
188
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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="LC188" class="line" lang="plaintext">fake1 5p + 14 0 1 2 0 3</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="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">fake1 5p + 15 0 2 0 1 3</span>
</pre>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">fake1 5p + 16 0 0 1 2 3</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">fake1 5p + 17 0 0 3 0 3</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">fake1 5p + 18 0 0 2 1 3</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">fake1 5p + 19 0 1 0 2 3</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">fake1 5p + 20 0 2 0 1 3</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">fake1 5p + 21 0 1 0 2 3</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">fake1 5p + 22 0 2 1 0 3</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">fake1 5p + 23 1 0 2 0 3</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">fake1 5p + 24 3 0 0 0 3</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">fake1 5p + 25 2 1 0 0 3</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">fake1 5p + 26 0 2 0 1 3</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">fake1 5p + 27 0 1 0 2 3</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">fake1 5p + 28 0 3 0 0 3</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">fake1 5p + 29 0 2 0 1 3</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">fake1 5p + 30 0 0 1 2 3</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">fake1 5p + 31 1 0 2 0 3</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">fake1 5p + 32 0 1 0 0 1</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">fake1 5p + 33 0 1 0 0 1</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">fake1 5p + 34 0 0 0 1 1</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">fake1 5p + 35 0 1 0 0 1</span>
</pre>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">fake1 5p + 36 1 0 0 0 1</span>
</pre>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">fake1 5p + 37 0 0 1 0 1</span>
</pre>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">fake1 5p + 38 1 0 0 0 1</span>
</pre>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">fake1 5p + 39 0 0 0 0 0</span>
</pre>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">fake1 5p + 40 0 0 0 0 0</span>
</pre>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">fake1 5p + 41 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">fake1 5p + 48 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">fake1 5p + 50 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">fake1 5p + 52 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">fake1 5p + 53 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">fake1 5p + 54 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">fake1 5p + 56 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">fake1 5p + 57 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">fake1 5p + 58 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">fake1 5p + 59 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">fake1 5p + 60 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">fake1 5p + 61 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">fake1 5p + 62 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">fake1 5p + 63 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">fake1 5p + 64 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">fake1 5p + 65 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">fake1 5p + 66 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">fake1 5p + 67 0 0 0 0 0</span>
</pre>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">fake1 5p + 68 0 0 0 0 0</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">fake1 5p + 69 0 0 0 0 0</span>
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<td class="diff-line-num new new_line" data-linenumber="244" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
244
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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="LC244" class="line" lang="plaintext">fake1 5p + 70 0 0 0 0 0</span>
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<td class="diff-line-num new new_line" data-linenumber="245" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
245
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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="LC245" class="line" lang="plaintext">fake1 5p - -10 0 3 1 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="246" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
246
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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="LC246" class="line" lang="plaintext">fake1 5p - -9 0 3 1 0 4</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="247" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
247
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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="LC247" class="line" lang="plaintext">fake1 5p - -8 3 0 1 0 4</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="248" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
248
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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="LC248" class="line" lang="plaintext">fake1 5p - -7 1 0 3 0 4</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="249" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
249
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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="LC249" class="line" lang="plaintext">fake1 5p - -6 0 3 1 0 4</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="250" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
250
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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="LC250" class="line" lang="plaintext">fake1 5p - -5 3 0 1 0 4</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="251" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
251
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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="LC251" class="line" lang="plaintext">fake1 5p - -4 0 4 0 0 4</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="252" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
252
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">fake1 5p - -3 0 0 0 4 4</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="253" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
253
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">fake1 5p - -2 0 0 1 3 4</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="254" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
254
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">fake1 5p - -1 1 0 0 3 4</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="255" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
255
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">fake1 5p - 1 0 0 4 0 4</span>
</pre>
</td>
</tr>
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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="256" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
256
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">fake1 5p - 2 1 0 3 0 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="257" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
257
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">fake1 5p - 3 0 1 3 0 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
258
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">fake1 5p - 4 2 0 2 0 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
259
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">fake1 5p - 5 0 0 4 0 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="260" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
260
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">fake1 5p - 6 0 0 4 0 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">fake1 5p - 7 0 3 0 1 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
262
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">fake1 5p - 8 1 0 0 3 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="263" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
263
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">fake1 5p - 9 3 0 1 0 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
264
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">fake1 5p - 10 4 0 0 0 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
265
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">fake1 5p - 11 0 0 3 1 4</span>
</pre>
</td>
</tr>
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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">
</td>
<td class="diff-line-num new new_line" data-linenumber="266" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
266
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">fake1 5p - 12 0 1 3 0 4</span>
</pre>
</td>
</tr>
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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="267" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">fake1 5p - 13 0 3 1 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">fake1 5p - 14 3 1 0 0 4</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">fake1 5p - 15 0 1 3 0 4</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">fake1 5p - 16 0 0 3 1 4</span>
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<td class="diff-line-num new new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">fake1 5p - 17 0 3 1 0 4</span>
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<td class="diff-line-num new new_line" data-linenumber="272" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
272
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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="LC272" class="line" lang="plaintext">fake1 5p - 18 4 0 0 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="273" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">fake1 5p - 19 0 0 4 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="274" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">fake1 5p - 20 3 0 1 0 4</span>
</pre>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">fake1 5p - 21 0 0 0 4 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="276" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">fake1 5p - 22 0 4 0 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">fake1 5p - 23 1 0 3 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="278" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
278
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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="LC278" class="line" lang="plaintext">fake1 5p - 24 0 2 1 1 4</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="279" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
279
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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="LC279" class="line" lang="plaintext">fake1 5p - 25 0 3 1 0 4</span>
</pre>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">fake1 5p - 26 1 0 0 3 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="281" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">fake1 5p - 27 0 0 4 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="282" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
282
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">fake1 5p - 28 3 0 0 1 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="283" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
283
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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="LC283" class="line" lang="plaintext">fake1 5p - 29 0 0 3 1 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="284" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
284
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">fake1 5p - 30 0 1 3 0 4</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="285" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
285
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">fake1 5p - 31 0 0 1 3 4</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="286" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
286
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">fake1 5p - 32 1 3 0 0 4</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="287" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
287
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">fake1 5p - 33 3 0 1 0 4</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="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
288
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">fake1 5p - 34 1 0 3 0 4</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="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
289
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">fake1 5p - 35 0 1 3 0 4</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="290" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
290
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">fake1 5p - 36 3 1 0 0 4</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="291" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
291
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">fake1 5p - 37 1 0 3 0 4</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="292" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
292
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">fake1 5p - 38 0 0 1 3 4</span>
</pre>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">fake1 5p - 39 0 1 0 3 4</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">fake1 5p - 40 0 3 0 1 4</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">fake1 5p - 41 0 1 3 0 4</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">fake1 5p - 42 3 0 0 0 3</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">fake1 5p - 43 0 0 3 0 3</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">fake1 5p - 44 3 0 0 0 3</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">fake1 5p - 45 0 3 0 0 3</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">fake1 5p - 46 0 3 0 0 3</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">fake1 5p - 47 2 0 1 0 3</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">fake1 5p - 48 0 0 3 0 3</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">fake1 5p - 49 0 3 0 0 3</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">fake1 5p - 50 0 3 0 0 3</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">fake1 5p - 51 0 0 0 3 3</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">fake1 5p - 52 0 0 0 0 0</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">fake1 5p - 53 0 0 0 0 0</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">fake1 5p - 54 0 0 0 0 0</span>
</pre>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">fake1 5p - 55 0 0 0 0 0</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">fake1 5p - 56 0 0 0 0 0</span>
</pre>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">fake1 5p - 57 0 0 0 0 0</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">fake1 5p - 58 0 0 0 0 0</span>
</pre>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">fake1 5p - 59 0 0 0 0 0</span>
</pre>
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314
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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="LC314" class="line" lang="plaintext">fake1 5p - 60 0 0 0 0 0</span>
</pre>
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315
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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="LC315" class="line" lang="plaintext">fake1 5p - 61 0 0 0 0 0</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="316" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
316
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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="LC316" class="line" lang="plaintext">fake1 5p - 62 0 0 0 0 0</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="317" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
317
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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="LC317" class="line" lang="plaintext">fake1 5p - 63 0 0 0 0 0</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="318" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">fake1 5p - 64 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">fake1 5p - 65 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">fake1 5p - 66 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">fake1 5p - 67 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">fake1 5p - 68 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">fake1 5p - 69 0 0 0 0 0</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">fake1 5p - 70 0 0 0 0 0</span></pre>
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<li id="eb01e35f66676b628c6352c0916f2b9979068834">
<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#eb01e35f66676b628c6352c0916f2b9979068834"><strong>mapdamage/tests/fake1.fasta</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">>fake1</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">GCTGGGATTACAGGTGCCTGCCACCACACCCAGCTAATTTTTGTATTTTTAGTAGAGATG</span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">GAGTTTCACCATGTCGGGCAGGCTGGTCTCGAACTCCTGACCTCAGGCGATCTGCCTGCC</span>
</pre>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">TCAGCCTCCCAAAGTGCTGGGATTACAGGCATGAGCTACCACGCCCGGTTCGCCAGTTGT</span>
</pre>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">TTTTTGATAGTATATAGAAAC</span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/compare/082127300ab8556a2e39232d06d300557539df7a...ac991c66c1eb17abed708778741089fed0ddd3f5#5b36c51c4f1b27b0dfac8bf20c1832cc35a4786d"><strong>mapdamage/tests/test.bam</strong></a>
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