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<h3>
Andreas Tille 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/48ed3c7fbfedc936cbd51e706c598de19dc7d6d9">48ed3c7f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-17T11:09:15Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.13.3</pre>
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<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<li class="file-stats">
<a href="#0fdbda66ca3b7b0b45b2a4108379ad19f7923a9e">
docs/bam_pipeline/configuration.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="#451ff695aa58ce88c0809c503d6a2377d398d218">
paleomix/nodes/validation.py
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<h4>Changes:</h4>
<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/paleomix/commit/48ed3c7fbfedc936cbd51e706c598de19dc7d6d9#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: #999;"># 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;">## [1.2.13.3] - 2018-11-01</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="p"> -</span> Fixed validation/read counting of pre-trimmed reads not including</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"> the mate 1 files of paired-end reads. This resulted in the</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown"> 'seq_retained_reads' count being half the expected value.</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>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.2.13.2] - 2018-04-22</span></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;">### Fixed</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="575" style="width: 35px; color: rgba(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">@@ -575,8 +581,9 @@ the (partially) updated documentation now hosted on ReadTheDocs.</td>
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<pre style="margin: 0;"> <span id="LC581" 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="LC582" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC583" class="line" lang="markdown"></span>
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<td class="diff-line-num old old_line" data-linenumber="578" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
578
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<pre style="margin: 0;">-<span id="LC578" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Unreleased</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...HEAD</span></span>
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<td class="diff-line-num old old_line" data-linenumber="579" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
579
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<pre style="margin: 0;">-<span id="LC579" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.1</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2</span></span>
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584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">Unreleased</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.3...HEAD</span></span>
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<td class="diff-line-num new new_line" data-linenumber="585" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.3</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.2...v1.2.13.3</span></span>
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.2</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13.1...v1.2.13.2</span></span>
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580
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<td class="diff-line-num new_line" data-linenumber="587" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC587" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13.1</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.13...v1.2.13.1</span></span>
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<pre style="margin: 0;"> <span id="LC588" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.13</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.12...v1.2.13</span></span>
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<pre style="margin: 0;"> <span id="LC589" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.2.12</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.11...v1.2.12</span></span>
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<a href="https://salsa.debian.org/med-team/paleomix/commit/48ed3c7fbfedc936cbd51e706c598de19dc7d6d9#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.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">@@ -14,4 +14,4 @@ The PALEOMIX pipelines have been published in Nature Protocols; if you make use</td>
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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">The Zonkey pipeline has been published in Journal of Archaeological Science; if you make use of this pipeline in your work, then please cite</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, and Orlando L. "**Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages**". Journal of Archaeological Science. 20<span class="idiff left right">0</span>7 Feb; 78:147-157. doi: `10.1016/j.jas.2016.12.005 <http://dx.doi.org/10.1016/j.jas.2016.12.005>`_. </span></pre>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Schubert M, Mashkour M, Gaunitz C, Fages A, Seguin-Orlando A, Sheikhi S, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Chuang R, Ermini L, Gamba C, Weinstock J, Vedat O, and Orlando L. "**Zonkey: A simple, accurate and sensitive pipeline to genetically identify equine F1-hybrids in archaeological assemblages**". Journal of Archaeological Science. 20<span class="idiff left right">1</span>7 Feb; 78:147-157. doi: `10.1016/j.jas.2016.12.005 <http://dx.doi.org/10.1016/j.jas.2016.12.005>`_. </span></pre>
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<a href="https://salsa.debian.org/med-team/paleomix/commit/48ed3c7fbfedc936cbd51e706c598de19dc7d6d9#0fdbda66ca3b7b0b45b2a4108379ad19f7923a9e"><strong>docs/bam_pipeline/configuration.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">@@ -9,7 +9,7 @@ The BAM pipeline exposes a number options, including the maximum number of threa</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">.. code-block:: bash</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext"> $ paleomix bam_pipeline --write-config</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> $ paleomix bam_pipeline <span class="idiff left right">run </span>--write-config</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">The resulting file contains a list of options which can be overwritten::</span>
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<a href="https://salsa.debian.org/med-team/paleomix/commit/48ed3c7fbfedc936cbd51e706c598de19dc7d6d9#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;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">13</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">2</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;">2</span><span class="p">,</span> <span class="mi" style="color: #099;">13</span><span class="p">,</span> <span class="mi" style="color: #099;"><span class="idiff left right">3</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;">'</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i.</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">i'</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">__version_info__</span></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>
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<a href="https://salsa.debian.org/med-team/paleomix/commit/48ed3c7fbfedc936cbd51e706c598de19dc7d6d9#451ff695aa58ce88c0809c503d6a2377d398d218"><strong>paleomix/nodes/validation.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">@@ -112,10 +112,10 @@ class ValidateFASTQFilesNode(Node):</td>
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<pre style="margin: 0;"> <span id="LC112" 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;">_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="python"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">read_type</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">input_files</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">iteritems</span><span class="p">():</span></span>
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">read_type</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"Paired"</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC115" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Pair</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">1</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC116" class="line" lang="python"> <span class="n" style="color: #333;"><span class="idiff left">filename</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Pair</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff right">2</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC117" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC118" 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;">_files</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">((</span><span class="n" style="color: #333;">read_type</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="LC115" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_files</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">add</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">read_type</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Pair</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">))</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="python"> <span class="bp" style="color: #999;"><span class="idiff left">self</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">_files</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">add</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">read_type</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">filename</span></span><span class="o" style="font-weight: 600;"><span class="idiff">.</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">format</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">Pair</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff right">))</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC117" 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="LC118" class="line" lang="python"> <span class="idiff left right"> </span><span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_files</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">add</span><span class="p">((</span><span class="n" style="color: #333;">read_type</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="LC119" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="python"> <span class="n" style="color: #333;">input_files</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[</span><span class="n" style="color: #333;">filename</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">filename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">_files</span><span class="p">]</span></span>
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<pre style="margin: 0;"> <span id="LC121" 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;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span></span>
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