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<h3>
Étienne Mollier pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/paleomix">Debian Med / paleomix</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7">6a3334d7</a></strong>
<div>
<span>by Étienne Mollier</span>
<i>at 2021-10-13T21:16:21+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.5</pre>
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<h4>8 changed files:</h4>
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#254a2da7a740675e537439eb88e32083b9ea4771">
docs/conf.py
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<li class="file-stats">
<a href="#5f751d21bc12129082e8f5d7b3edbc140a238ce7">
docs/installation.rst
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<li class="file-stats">
<a href="#31db6545668043f26d9d05b8338b53acf3b3c5e1">
paleomix/__init__.py
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<li class="file-stats">
<a href="#35084866572fc8e1ab7482ea5fe0b7a9d2713816">
paleomix/pipelines/bam/config.py
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<li class="file-stats">
<a href="#b75ef46222df83cc5e8394f0243adc5094e3b441">
paleomix/pipelines/bam/nodes.py
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<li class="file-stats">
<a href="#c5e998f5e10875027e73c40bd9d87d2c82707e9a">
paleomix/pipelines/bam/parts/prefix.py
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<li class="file-stats">
<a href="#05b9434c6f6c420942ce278e6fed40fa39b01fe1">
paleomix_environment.yaml
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #800080; font-weight: 600;"># Changelog</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="gu" style="color: #800080; font-weight: 600;">## [1.3.5] - 2021-10-12</span></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="gu" style="color: #800080; font-weight: 600;">### Added</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p"> -</span> Added command-line option to reduce/turn off validation with picard ValidateSamFile.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.3.4] - 2021-09-23</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="LC11" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Added</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="752" style="width: 35px; color: rgba(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="758" style="width: 35px; color: rgba(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">@@ -752,8 +758,8 @@ the (partially) updated documentation now hosted on ReadTheDocs.</td>
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758
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<pre style="margin: 0;"> <span id="LC758" class="line" lang="markdown"><span class="p"> -</span> Switching to more traditional version-number tracking.</span>
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<pre style="margin: 0;"> <span id="LC759" class="line" lang="markdown"></span>
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754
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760
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<pre style="margin: 0;"> <span id="LC760" class="line" lang="markdown"></span>
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<td class="old_line diff-line-num old" data-linenumber="755" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
755
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<td class="new_line diff-line-num old" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC755" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;"><span class="idiff left">Unreleased</span></span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.3.4...<span class="idiff right">HEAD</span></span></span>
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<td class="old_line diff-line-num old" data-linenumber="756" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
756
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<td class="new_line diff-line-num old" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC756" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.3.<span class="idiff left right">3</span></span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.3.3...v1.3.4</span></span>
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<td class="new_line diff-line-num new" data-linenumber="761" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;"><span class="idiff left">1.3.5</span></span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.3.4...<span class="idiff right">v1.3.5</span></span></span>
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<td class="old_line diff-line-num new" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="762" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.3.<span class="idiff left right">4</span></span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.3.3...v1.3.4</span></span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="757" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
757
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<td class="new_line diff-line-num" data-linenumber="763" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
763
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<pre style="margin: 0;"> <span id="LC763" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.3.3</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.3.2...v1.3.3</span></span>
</pre>
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758
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<td class="new_line diff-line-num" data-linenumber="764" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
764
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<pre style="margin: 0;"> <span id="LC764" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.3.2</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.3.1...v1.3.2</span></span>
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<pre style="margin: 0;"> <span id="LC765" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.3.1</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.3.0...v1.3.1</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7#254a2da7a740675e537439eb88e32083b9ea4771"><strong>docs/conf.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">@@ -26,7 +26,7 @@ author = "Mikkel Schubert"</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The short X.Y version</span></span>
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<pre style="margin: 0;"> <span id="LC27" 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;">"1.3"</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;"># The full version, including alpha/beta/rc tags</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.3.<span class="idiff left right">4</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"1.3.<span class="idiff left right">5</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"></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;"># -- General configuration ---------------------------------------------------</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7#5f751d21bc12129082e8f5d7b3edbc140a238ce7"><strong>docs/installation.rst</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">@@ -17,13 +17,13 @@ In addition, some libraries used by PALEOMIX may require additional development</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">Once all requirements have been installed, PALEOMIX may be installed using `pip`::</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> $ python3 -m pip install paleomix==1.3.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> $ python3 -m pip install paleomix==1.3.<span class="idiff left right">5</span></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">To verify that the installation was carried out correctly, run the command `paleomix`::</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> $ paleomix</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> PALEOMIX - pipelines and tools for NGS data analyses</span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext"> Version: v1.3.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> Version: v1.3.<span class="idiff left right">5</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> ...</span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext"></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">@@ -45,7 +45,7 @@ This installation method requires the `venv` module. On Debian based systems, th</td>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">Once `venv` is installed, creation of a virtual environment and installation of PALEOMIX may be carried out as shown here::</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"> $ python3 -m venv venv</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext"> $ ./venv/bin/pip install paleomix==v1.3.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> $ ./venv/bin/pip install paleomix==v1.3.<span class="idiff left right">5</span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="plaintext">Following successful completion of these commands, the `paleomix` executable will be accessible in the `./venv/bin/` folder. However, as this folder also contains a copy of Python itself, it is not recommended to add it to your `PATH`. Instead, simply link the `paleomix` executable to a folder in your `PATH`. This can be accomplished as follows::</span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></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">@@ -78,7 +78,7 @@ To install `conda` and also set it up so it can use the `bioconda`_ bioinformati</td>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="plaintext">Next, run the following commands to download the conda environment template for this release of PALEOMIX and to create a new conda environment named `paleomix` using that template::</span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="plaintext"> $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.<span class="idiff left right">4</span>/paleomix_environment.yaml > paleomix_environment.yaml</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> $ curl -fL https://github.com/MikkelSchubert/paleomix/releases/download/v1.3.<span class="idiff left right">5</span>/paleomix_environment.yaml > paleomix_environment.yaml</span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="plaintext"> $ conda env create -n paleomix -f paleomix_environment.yaml</span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="plaintext">You can now activate the paleomix environment with::</span>
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<li id="31db6545668043f26d9d05b8338b53acf3b3c5e1">
<a href="https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7#31db6545668043f26d9d05b8338b53acf3b3c5e1"><strong>paleomix/__init__.py</strong></a>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># SOFTWARE.</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;">#</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">__version_info__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">4</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="python"><span class="n" style="color: #333;">__version_info__</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">5</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" 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;">"%i.%i.%i"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">__version_info__</span></span></pre>
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<a href="https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7#35084866572fc8e1ab7482ea5fe0b7a9d2713816"><strong>paleomix/pipelines/bam/config.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">@@ -166,6 +166,18 @@ def add_run_command(subparsers):</td>
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<pre style="margin: 0;"> <span id="LC166" class="line" lang="python"> <span class="s" style="color: #d14;">"to the JRE (Jave Runtime Environment); e.g. to change the "</span></span>
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167
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<pre style="margin: 0;"> <span id="LC167" class="line" lang="python"> <span class="s" style="color: #d14;">"maximum amount of memory (default is -Xmx4g)"</span><span class="p">,</span></span>
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168
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">group</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="python"> <span class="s" style="color: #d14;">"--validation"</span><span class="p">,</span></span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">metavar</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"LEVEL"</span><span class="p">,</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="python"> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">str</span><span class="p">.</span><span class="n" style="color: #333;">lower</span><span class="p">,</span></span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="python"> <span class="n" style="color: #333;">choices</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"off"</span><span class="p">,</span> <span class="s" style="color: #d14;">"partial"</span><span class="p">,</span> <span class="s" style="color: #d14;">"full"</span><span class="p">),</span></span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="python"> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"full"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"Change the amount of validation performed using picard ValidateSamFile. "</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python"> <span class="s" style="color: #d14;">"Set to 'full' to validate both intermediate and final BAM files; set to "</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python"> <span class="s" style="color: #d14;">"'partial' to validate only the final BAM files; and set to 'off' to disable "</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python"> <span class="s" style="color: #d14;">"validation. Reducing the amount of validation may greatly decrease the total "</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="python"> <span class="s" style="color: #d14;">"runtime"</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="python"> <span class="p">)</span></span>
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"></span>
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170
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Removed options</span></span>
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171
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">"--gatk-max-threads"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">SUPPRESS</span><span class="p">)</span></span>
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<li id="b75ef46222df83cc5e8394f0243adc5094e3b441">
<a href="https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7#b75ef46222df83cc5e8394f0243adc5094e3b441"><strong>paleomix/pipelines/bam/nodes.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">@@ -24,7 +24,14 @@ from paleomix.nodes.picard import ValidateBAMNode</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">paleomix.nodes.samtools</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">BAMIndexNode</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">index_and_validate_bam</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span> <span class="n" style="color: #333;">create_index</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="LC27" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">index_and_validate_bam</span><span class="p">(</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">None</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="python"> <span class="n" style="color: #333;">create_index</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="LC33" class="line" lang="python"> <span class="n" style="color: #333;">validation_levels</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"full"</span><span class="p">,),</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="python"><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="python"> <span class="n" style="color: #333;">input_file</span><span class="p">,</span> <span class="n" style="color: #333;">index_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">_get_input_files</span><span class="p">(</span><span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">[</span><span class="s" style="color: #d14;">"IndexFormat"</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;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">index_file</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">create_index</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="python"> <span class="n" style="color: #333;">node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">BAMIndexNode</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">@@ -32,6 +39,10 @@ def index_and_validate_bam(config, prefix, node, log_file=None, create_index=Tru</td>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">index_file</span><span class="p">,)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">node</span><span class="p">.</span><span class="n" style="color: #333;">output_files</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Only enable validation if the user picked a corresponding level</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">config</span><span class="p">.</span><span class="n" style="color: #333;">validation</span> <span class="ow" style="font-weight: 600;">not</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">validation_levels</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">node</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="n" style="color: #333;">ignored_checks</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Ignored since we may filter out misses and low-quality hits during</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># mapping, which leads to a large proportion of missing PE mates.</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7#c5e998f5e10875027e73c40bd9d87d2c82707e9a"><strong>paleomix/pipelines/bam/parts/prefix.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">@@ -24,8 +24,8 @@ import os</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">paleomix.common.utilities</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">safe_coerce_to_tuple</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">paleomix.nodes.picard</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">MergeSamFilesNode</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">paleomix.pipelines.bam.nodes</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">index_and_validate_bam</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">paleomix.nodes.validation</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">DetectInputDuplicationNode</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">paleomix.pipelines.bam.nodes</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">index_and_validate_bam</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">Prefix</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">@@ -64,7 +64,11 @@ class Prefix:</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">dependencies</span><span class="o" style="font-weight: 600;">=</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">datadup_check</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">validated_node</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">index_and_validate_bam</span><span class="p">(</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">node</span><span class="p">,</span> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">validated_filename</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="python"> <span class="n" style="color: #333;">config</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">config</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">prefix</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">prefix</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">node</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">node</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="python"> <span class="n" style="color: #333;">log_file</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">validated_filename</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="python"> <span class="n" style="color: #333;">validation_levels</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"full"</span><span class="p">,</span> <span class="s" style="color: #d14;">"partial"</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"> <span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">{</span><span class="n" style="color: #333;">output_filename</span><span class="p">:</span> <span class="n" style="color: #333;">validated_node</span><span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/-/commit/6a3334d70c7ce4934c448dc02b3e3e9f353bc5d7#05b9434c6f6c420942ce278e6fed40fa39b01fe1"><strong>paleomix_environment.yaml</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">@@ -17,4 +17,4 @@ dependencies:</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">r-gam</span></span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">r-inline</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">pip</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">paleomix==1.3.<span class="idiff left right">4</span></span></span></pre>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">paleomix==1.3.<span class="idiff left right">5</span></span></span></pre>
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