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<h3>
Steffen Möller pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/mapdamage">Debian Med / mapdamage</a>
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<h4>
Commits:
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<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/mapdamage/-/commit/a9e55a3f0ab6028446b146672cdcd8fa1f045427">a9e55a3f</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-06-30T00:19:26+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.2.1+dfsg</pre>
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<h4>4 changed files:</h4>
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<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="#65134f9708e381a1019a789ae57129129e967d80">
mapdamage/version.py
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<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
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<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/mapdamage/-/commit/a9e55a3f0ab6028446b146672cdcd8fa1f045427#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## mapDamage</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/mapdamage2/README.html) <span class="p">[</span><span class="nv" style="color: #008080;">![Conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/mapdamage2.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/mapdamage2/files) <span class="idiff left">!</span><span class="p"><span class="idiff">[</span></span><span class="nv" style="color: #008080;"><span class="idiff">Conda</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://anaconda.org/bioconda/mapdamage2/badges/latest_release_date.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">![</span></span><span class="nv" style="color: #008080;"><span class="idiff">Conda</span></span><span class="p"><span class="idiff">](</span></span><span class="sx" style="color: #d14;"><span class="idiff">https://anaconda.org/bioconda/mapdamage2/badges/version.svg</span></span><span class="p"><span class="idiff">)</span></span><span class="idiff"> </span><span class="p"><span class="idiff">[</span></span><span class="ss" style="color: #990073;"><span class="idiff">![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff right">(https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">![install with bioconda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat</span><span class="p">)</span>](http://bioconda.github.io/recipes/mapdamage2/README.html) <span class="p">[</span><span class="nv" style="color: #008080;">![Conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://img.shields.io/conda/dn/bioconda/mapdamage2.svg</span><span class="p">)</span>](https://anaconda.org/bioconda/mapdamage2/files) </span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p">![</span><span class="nv" style="color: #008080;">Conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/mapdamage2/badges/latest_release_date.svg</span><span class="p">)</span> <span class="p">![</span><span class="nv" style="color: #008080;">Conda</span><span class="p">](</span><span class="sx" style="color: #d14;">https://anaconda.org/bioconda/mapdamage2/badges/version.svg</span><span class="p">)</span> <span class="p">[</span><span class="ss" style="color: #990073;">![Project Status: Inactive – The project has reached a stable, usable state but is no longer being actively developed; support/maintenance will be provided as time allows.</span><span class="p">]</span>(https://www.repostatus.org/badges/latest/inactive.svg)](https://www.repostatus.org/#inactive)</span>
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5
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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;">#### `bioconda` installation</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<td class="diff-line-num new_line old" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="markdown"><span class="p">-</span> python3 version <span class="gs" style="font-weight: 600;">**2.2.0**</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="markdown">conda install -c bioconda mapdamage2=2.2.0</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> python3 version <span class="gs" style="font-weight: 600;">**2.2.1**</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="markdown"><span class="p">-</span> python3 version <span class="gs" style="font-weight: 600;">**2.2.0**</span> <span class="gs" style="font-weight: 600;">**with**</span> R and 4 mandatory packages for the Bayesian inference:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"><span class="p">```</span><span class="nl"> </span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown">conda install -c bioconda mapdamage2=2.2.1</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="markdown">conda install -c bioconda mapdamage2=2.2.0=pyr36_1</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="markdown"><span class="p">*</span> python3 version <span class="gs" style="font-weight: 600;">**2.2.1**</span> <span class="gs" style="font-weight: 600;">**with**</span> R and 4 mandatory packages for the Bayesian inference:</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="markdown"><span class="p">```</span><span class="nl"> </span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="markdown">conda install -c bioconda mapdamage2=2.2.1=pyr36_1</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="markdown"><span class="p">---</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Important</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="markdown"></span>
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22
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="markdown"><span class="p"><span class="idiff left">-</span></span><span class="idiff"> From version </span><span class="sb" style="color: #d14;"><span class="idiff right">`2.2.0</span>`</span> the <span class="sb" style="color: #d14;">`master`</span> branch is requiring <span class="gs" style="font-weight: 600;">**python3**</span> as <span class="sb" style="color: #d14;">`python2`</span> is not supported from 2020-01-01.</span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="markdown"><span class="p"><span class="idiff left">*</span></span><span class="idiff"> From version </span><span class="sb" style="color: #d14;"><span class="idiff right">`2.2.1</span>`</span> the <span class="sb" style="color: #d14;">`master`</span> branch is requiring <span class="gs" style="font-weight: 600;">**python3**</span> as <span class="sb" style="color: #d14;">`python2`</span> is not supported from 2020-01-01.</span>
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23
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="markdown"><span class="p"><span class="idiff left right">-</span></span> Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of <span class="sb" style="color: #d14;">`mapDamage`</span> to use half of the data for estimation of the damage parameters, sorry for the inconvenience.</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="markdown"><span class="p"><span class="idiff left right">*</span></span> Users with versions dating prior to June 12 2013 please update. A nasty bug that caused the statistical part of <span class="sb" style="color: #d14;">`mapDamage`</span> to use half of the data for estimation of the damage parameters, sorry for the inconvenience.</span>
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25
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC29" 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="LC30" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="markdown">Complete documentation, instructions, examples, screenshots and FAQ are available at <span class="p">[</span><span class="nv" style="color: #008080;">this address</span><span class="p">](</span><span class="sx" style="color: #d14;">http://ginolhac.github.io/mapDamage/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC33" 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;">https://geogenetics.ku.dk/publications/mapdamage2.0/</span><span class="p">)</span> is a computational framework written in <span class="gs" style="font-weight: 600;">**Python3**</span> and <span class="gs" style="font-weight: 600;">**R**</span>, which tracks and quantifies DNA damage patterns</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,31 +35,30 @@ among ancient DNA sequencing reads generated by Next-Generation Sequencing platf</td>
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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="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;">https://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;">https://geogenetics.ku.dk/research_groups/palaeomix_group/</span><span class="p">)</span>.</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Citation</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="markdown">If you use this program, please cite the following publication: </span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="markdown">Jónsson H, Ginolhac A, Schubert M, Johnson P, Orlando L.</span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters.</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="markdown"><span class="nv" style="color: #008080;">_Bioinformatics_ 23rd April 2013. doi: 10.1093/bioinformatics/btt193</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bioinformatics.oxfordjournals.org/content/early/2013/05/17/bioinformatics.btt193</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC44" 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="LC45" class="line" lang="markdown">The original <span class="sb" style="color: #d14;">`mapDamage1`</span> was published in the following article: </span>
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<pre style="margin: 0;"> <span id="LC46" 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="LC47" class="line" lang="markdown"><span class="p">[</span><span class="nv" style="color: #008080;">mapDamage: testing for damage patterns in ancient DNA sequences. _Bioinformatics_ 2011 **27**(15):2153-5</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="markdown"><span class="nv" style="color: #008080;">http://bioinformatics.oxfordjournals.org/content/27/15/2153</span><span class="p">](</span><span class="sx" style="color: #d14;">http://bioinformatics.oxfordjournals.org/content/27/15/2153</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Test the no-stats part and rescaling</span></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="markdown">you can test <span class="sb" style="color: #d14;">`mapDamage`</span> by running:</span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="markdown"></span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="markdown"><span class="p">```</span><span class="nl"><span class="idiff left right"> </span></span></span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="markdown">cd mapDamage/mapdamage/</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="markdown">python3 mp_test.py</span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="markdown"></span>
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59
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="markdown">should return</span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="markdown"><span class="p">```</span><span class="nl"> </span></span>
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59
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="markdown">Started with the command: /usr/local/bin/mapDamage -i tests/test.bam -r tests/fake1.fasta -d tests/results --no-stats</span>
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60
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="markdown"> Reading from 'tests/test.bam'</span>
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61
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="markdown"> Writing results to 'tests/results/'</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="72" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -69,7 +72,7 @@ Ran 2 tests in 3.357s</td>
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69
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="markdown">OK</span>
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70
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73
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="markdown"><span class="p">```</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="markdown"></span>
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72
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="markdown"></span>
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73
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<pre style="margin: 0;"> <span id="LC75" 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="LC76" class="line" lang="markdown"></span>
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74
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<pre style="margin: 0;"> <span id="LC77" 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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75
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="markdown">ginolhac at gmail.com, mikkelsch at gmail.com or jonsson.hakon at gmail.com.</span></pre>
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<li id="806a2eb8d45517373c81701d49fefdfd30e648c5">
<a href="https://salsa.debian.org/med-team/mapdamage/-/commit/a9e55a3f0ab6028446b146672cdcd8fa1f045427#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">@@ -139,20 +139,6 @@ 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=%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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141
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="python"></span>
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142
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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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143
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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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144
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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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<pre style="margin: 0;">-<span id="LC146" class="line" lang="python"><span class="s" style="color: #d14;"> """</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="python"></span>
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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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<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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<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="p">.</span><span class="n" style="color: #333;">is_paired</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="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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<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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<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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<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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<pre style="margin: 0;">-<span id="LC155" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC142" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python"><span class="k" style="font-weight: 600;">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="LC144" 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="p">.</span><span class="n" style="color: #333;">time</span><span class="p">()</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="241" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -241,14 +227,6 @@ def main():</td>
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<pre style="margin: 0;"> <span id="LC227" 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="LC228" class="line" lang="python"> <span class="n" style="color: #333;">in_bam</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pysam</span><span class="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">options</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="LC229" 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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<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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246
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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="p">.</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="p">.</span><span class="n" style="color: #333;">stderr</span><span class="p">.</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="p">.</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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<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="p">.</span><span class="n" style="color: #333;">Samfile</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">filename</span><span class="p">)</span></span>
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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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252
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230
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<pre style="margin: 0;"> <span id="LC230" 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="p">.</span><span class="n" style="color: #333;">references</span><span class="p">,</span> <span class="n" style="color: #333;">in_bam</span><span class="p">.</span><span class="n" style="color: #333;">lengths</span><span class="p">)))</span></span>
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253
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231
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<pre style="margin: 0;"> <span id="LC231" 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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254
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232
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python"> <span class="n" style="color: #333;">fai_lengths</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">mapdamage</span><span class="p">.</span><span class="n" style="color: #333;">seq</span><span class="p">.</span><span class="n" style="color: #333;">read_fasta_index</span><span class="p">(</span><span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">ref</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">".fai"</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/mapdamage/-/commit/a9e55a3f0ab6028446b146672cdcd8fa1f045427#65134f9708e381a1019a789ae57129129e967d80"><strong>mapdamage/version.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,4 +2,4 @@</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="k" style="font-weight: 600;">try</span><span class="p">:</span></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"> <span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">mapdamage._version</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">__version__</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="k" style="font-weight: 600;">except</span> <span class="nb" style="color: #0086b3;">ImportError</span><span class="p">:</span></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.2.<span class="idiff left right">0</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"> <span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"2.2.<span class="idiff left right">1</span>"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/mapdamage/-/commit/a9e55a3f0ab6028446b146672cdcd8fa1f045427#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -35,7 +35,7 @@ def setup_version():</td>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">check_output</span><span class="p">((</span><span class="s" style="color: #d14;">"git"</span><span class="p">,</span> <span class="s" style="color: #d14;">"describe"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--always"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--tags"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--dirty"</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="python"> <span class="k" style="font-weight: 600;">with</span> <span class="nb" style="color: #0086b3;">open</span><span class="p">(</span><span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">path</span><span class="p">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="s" style="color: #d14;">"mapdamage"</span><span class="p">,</span> <span class="s" style="color: #d14;">"_version.py"</span><span class="p">),</span> <span class="s" style="color: #d14;">"w"</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">handle</span><span class="p">:</span></span>
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">handle</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"#!/usr/bin/env python</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">)</span></span>
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38
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<pre style="margin: 0;">-<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">handle</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"__version__ = %r</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">.</span><span class="n" style="color: #333;">strip</span><span class="p">(),))</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="python"> <span class="n" style="color: #333;">handle</span><span class="p">.</span><span class="n" style="color: #333;">write</span><span class="p">(</span><span class="s" style="color: #d14;">"__version__ = %r</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">version</span><span class="p">.</span><span class="n" style="color: #333;"><span class="idiff left">decode</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">"utf-8"</span></span><span class="p"><span class="idiff right">).</span></span><span class="n" style="color: #333;">strip</span><span class="p">(),))</span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="k" style="font-weight: 600;">except</span> <span class="p">(</span><span class="n" style="color: #333;">subprocess</span><span class="p">.</span><span class="n" style="color: #333;">CalledProcessError</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">OSError</span><span class="p">)</span> <span class="k" style="font-weight: 600;">as</span> <span class="n" style="color: #333;">error</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="k" style="font-weight: 600;">raise</span> <span class="nb" style="color: #0086b3;">SystemExit</span><span class="p">(</span><span class="s" style="color: #d14;">"Could not determine mapDamage version: %s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">error</span><span class="p">,))</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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