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GitLab

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<h3>

Étienne Mollier pushed to branch master

at <a href="https://salsa.debian.org/med-team/paleomix">Debian Med / paleomix</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/67476a8c86dd32b73918367fd5095aa643732a0a">67476a8c</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2021-12-11T21:22:59+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/4ecb3fd49faf45b0f56280eb42f5af47f1fdfc77">4ecb3fd4</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2021-12-11T21:23:00+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.6</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/0fcd63e5ff423d711409ddaa0e014868c6b7a1f4">0fcd63e5</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2021-12-11T21:23:06+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/1.3.6'

Update to upstream version '1.3.6'

with Debian dir a522019c57d3cc7aae9a28615b07e5d24f058326</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/d27cf3fbffff3e29b7ebd39dcb05357c64a780b3">d27cf3fb</a></strong>

<div>

<span>by Étienne Mollier</span>

<i>at 2021-12-11T21:26:55+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable

</pre>

</li>

</ul>

<h4>8 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">

CHANGES.md

</a>

</li>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#254a2da7a740675e537439eb88e32083b9ea4771">

docs/conf.py

</a>

</li>

<li class="file-stats">

<a href="#5f751d21bc12129082e8f5d7b3edbc140a238ce7">

docs/installation.rst

</a>

</li>

<li class="file-stats">

<a href="#31db6545668043f26d9d05b8338b53acf3b3c5e1">

paleomix/__init__.py

</a>

</li>

<li class="file-stats">

<a href="#26d079b57f7dd8b3721b11d5d3434dccad261530">

paleomix/nodes/adapterremoval.py

</a>

</li>

<li class="file-stats">

<a href="#2124c1b886aa0bf818b7d436e9355b0d72a49e19">

paleomix/pipelines/bam/makefile.py

</a>

</li>

<li class="file-stats">

<a href="#05b9434c6f6c420942ce278e6fed40fa39b01fe1">

paleomix_environment.yaml

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">

<a href="https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>

<hr>

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1

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1

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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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="2" 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">

2

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<td class="new_line diff-line-num" data-linenumber="2" 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">

2

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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">

<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.3.6] - 2021-11-28</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

4

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC4" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

5

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Added</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC6" class="line" lang="markdown"><span class="p">  -</span> Added explicit support for the AdapterRemoval <span class="sb" style="color: #d14;">`--trim5p`</span> and <span class="sb" style="color: #d14;">`--trim3p`</span> options,</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="7" 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">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="markdown">    which may take one or two values (as a list).</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

9

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Changed</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"><span class="p">  -</span> User options for AdapterRemoval are no longer restricted by a whitelist.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC11" class="line" lang="markdown"></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="12" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC12" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="3" 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">

3

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<td class="new_line diff-line-num" data-linenumber="13" 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="LC13" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.3.5] - 2021-10-12</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="4" 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">

4

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<td class="new_line diff-line-num" data-linenumber="14" 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="LC14" class="line" lang="markdown"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="5" 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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<td class="new_line diff-line-num" data-linenumber="15" 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="LC15" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Added</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_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>

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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">@@ -758,6 +768,7 @@ the (partially) updated documentation now hosted on ReadTheDocs.</td>

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758

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<pre style="margin: 0;"> <span id="LC768" class="line" lang="markdown"><span class="p">  -</span> Switching to more traditional version-number tracking.</span>

</pre>

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769

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<pre style="margin: 0;"> <span id="LC769" class="line" lang="markdown"></span>

</pre>

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760

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<td class="new_line diff-line-num" data-linenumber="770" 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">

770

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<pre style="margin: 0;"> <span id="LC770" class="line" lang="markdown"></span>

</pre>

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<td class="old_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">

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<td class="new_line diff-line-num new" data-linenumber="771" 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">

771

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<pre style="margin: 0;">+<span id="LC771" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.3.6</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.3.5...v1.3.6</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="761" 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">

761

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<td class="new_line diff-line-num" data-linenumber="772" 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="LC772" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.3.5</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.3.4...v1.3.5</span></span>

</pre>

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762

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<td class="new_line diff-line-num" data-linenumber="773" 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">

773

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<pre style="margin: 0;"> <span id="LC773" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.3.4</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="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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<td class="new_line diff-line-num" data-linenumber="774" 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">

774

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<pre style="margin: 0;"> <span id="LC774" 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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<br>

</li>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">paleomix (1.3.6-1) unstable; urgency=medium</span>

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * New upstream version</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Étienne Mollier <emollier@debian.org>  Sat, 11 Dec 2021 21:23:21 +0100</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>

</pre>

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1

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7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">paleomix (1.3.5-1) unstable; urgency=medium</span>

</pre>

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2

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8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"></span>

</pre>

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3

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<td class="new_line diff-line-num" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * New upstream version</span>

</pre>

</td>

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<br>

</li>

<li id="254a2da7a740675e537439eb88e32083b9ea4771">

<a href="https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3#254a2da7a740675e537439eb88e32083b9ea4771"><strong>docs/conf.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="26" 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="26" 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">@@ -26,7 +26,7 @@ author = "Mikkel Schubert"</td>

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<td class="old_line diff-line-num" data-linenumber="26" 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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<td class="new_line diff-line-num" data-linenumber="26" 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="LC26" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The short X.Y version</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="27" 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="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>

</pre>

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<td class="old_line diff-line-num" data-linenumber="28" 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">

28

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<td class="new_line diff-line-num" data-linenumber="28" 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="LC28" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full version, including alpha/beta/rc tags</span></span>

</pre>

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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="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">6</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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<li id="5f751d21bc12129082e8f5d7b3edbc140a238ce7">

<a href="https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3#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">5</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">6</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">5</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">6</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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<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">5</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">6</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>

</pre>

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<pre style="margin: 0;"> <span id="LC51" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" 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="78" 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">@@ -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">5</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">6</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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<br>

</li>

<li id="31db6545668043f26d9d05b8338b53acf3b3c5e1">

<a href="https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3#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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22

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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>

</pre>

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23

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<td class="new_line diff-line-num" data-linenumber="23" 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">

23

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="24" 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">

24

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<td class="new_line diff-line-num old" data-linenumber="24" 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="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>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="25" 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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="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">6</span></span><span class="p">)</span></span>

</pre>

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25

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<td class="new_line diff-line-num" data-linenumber="25" 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">

25

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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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<br>

</li>

<li id="26d079b57f7dd8b3721b11d5d3434dccad261530">

<a href="https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3#26d079b57f7dd8b3721b11d5d3434dccad261530"><strong>paleomix/nodes/adapterremoval.py</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="142" 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="142" 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">@@ -142,4 +142,14 @@ def _get_common_parameters(options, threads=1):</td>

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142

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<td class="new_line diff-line-num" data-linenumber="142" 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="LC142" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">set_option</span><span class="p">(</span><span class="s" style="color: #d14;">"--adapter-list"</span><span class="p">,</span> <span class="s" style="color: #d14;">"%(IN_ADAPTER_LIST)s"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="143" 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">

143

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<td class="new_line diff-line-num" data-linenumber="143" 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">

143

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="python">        <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">command</span><span class="p">.</span><span class="n" style="color: #333;">set_kwargs</span><span class="p">(</span><span class="n" style="color: #333;">IN_ADAPTER_LIST</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">adapter_list</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="144" 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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<td class="new_line diff-line-num" data-linenumber="144" 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="LC144" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="p">(</span><span class="s" style="color: #d14;">"--trim5p"</span><span class="p">,</span> <span class="s" style="color: #d14;">"--trim3p"</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="146" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="python">        <span class="n" style="color: #333;">values</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">options</span><span class="p">.</span><span class="n" style="color: #333;">pop</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="bp" style="color: #999;">None</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="147" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">values</span> <span class="ow" style="font-weight: 600;">is</span> <span class="ow" style="font-weight: 600;">not</span> <span class="bp" style="color: #999;">None</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="python">            <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add_value</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="149" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC149" class="line" lang="python">            <span class="k" style="font-weight: 600;">if</span> <span class="nb" style="color: #0086b3;">isinstance</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">list</span><span class="p">):</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="150" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC150" class="line" lang="python">                <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">value</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">values</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="151" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC151" class="line" lang="python">                    <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add_value</span><span class="p">(</span><span class="n" style="color: #333;">value</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="152" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC152" class="line" lang="python">            <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="145" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="153" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC153" class="line" lang="python">                <span class="n" style="color: #333;">cmd</span><span class="p">.</span><span class="n" style="color: #333;">add_value</span><span class="p">(</span><span class="n" style="color: #333;">values</span><span class="p">)</span></span>

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<td class="new_line diff-line-num new" data-linenumber="154" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC154" class="line" lang="python"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC155" class="line" lang="python">    <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">cmd</span></span></pre>

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<br>

</li>

<li id="2124c1b886aa0bf818b7d436e9355b0d72a49e19">

<a href="https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3#2124c1b886aa0bf818b7d436e9355b0d72a49e19"><strong>paleomix/pipelines/bam/makefile.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="173" 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="173" 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">@@ -173,6 +173,9 @@ _VALIDATION_OPTIONS = {</td>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python">        <span class="s" style="color: #d14;">"--preserve5p"</span><span class="p">:</span> <span class="n" style="color: #333;">Or</span><span class="p">(</span><span class="n" style="color: #333;">IsNone</span><span class="p">,</span> <span class="n" style="color: #333;">IsBoolean</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python">        <span class="s" style="color: #d14;">"--collapse-deterministic"</span><span class="p">:</span> <span class="n" style="color: #333;">Or</span><span class="p">(</span><span class="n" style="color: #333;">IsNone</span><span class="p">,</span> <span class="n" style="color: #333;">IsBoolean</span><span class="p">),</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="175" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="python">        <span class="s" style="color: #d14;">"--collapse-conservatively"</span><span class="p">:</span> <span class="n" style="color: #333;">Or</span><span class="p">(</span><span class="n" style="color: #333;">IsNone</span><span class="p">,</span> <span class="n" style="color: #333;">IsBoolean</span><span class="p">),</span></span>

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<pre style="margin: 0;">+<span id="LC176" class="line" lang="python">        <span class="s" style="color: #d14;">"--trim5p"</span><span class="p">:</span> <span class="n" style="color: #333;">Or</span><span class="p">(</span><span class="n" style="color: #333;">IsInt</span><span class="p">,</span> <span class="n" style="color: #333;">IsListOf</span><span class="p">(</span><span class="n" style="color: #333;">IsInt</span><span class="p">)),</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="177" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC177" class="line" lang="python">        <span class="s" style="color: #d14;">"--trim3p"</span><span class="p">:</span> <span class="n" style="color: #333;">Or</span><span class="p">(</span><span class="n" style="color: #333;">IsInt</span><span class="p">,</span> <span class="n" style="color: #333;">IsListOf</span><span class="p">(</span><span class="n" style="color: #333;">IsInt</span><span class="p">)),</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="178" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC178" class="line" lang="python">        <span class="n" style="color: #333;">StringStartsWith</span><span class="p">(</span><span class="s" style="color: #d14;">"--"</span><span class="p">):</span> <span class="n" style="color: #333;">Or</span><span class="p">(</span><span class="n" style="color: #333;">IsStr</span><span class="p">,</span> <span class="n" style="color: #333;">IsInt</span><span class="p">,</span> <span class="n" style="color: #333;">IsFloat</span><span class="p">,</span> <span class="n" style="color: #333;">IsNone</span><span class="p">),</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="python">    <span class="p">},</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python">    <span class="c1" style="color: #998; font-style: italic;"># Which aliger/mapper to use (BWA/Bowtie2)</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python">    <span class="s" style="color: #d14;">"Aligners"</span><span class="p">:</span> <span class="p">{</span></span>

</pre>

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<br>

</li>

<li id="05b9434c6f6c420942ce278e6fed40fa39b01fe1">

<a href="https://salsa.debian.org/med-team/paleomix/-/compare/9f14424d8136cbc2755dba4d6fd4790f6580f84b...d27cf3fbffff3e29b7ebd39dcb05357c64a780b3#05b9434c6f6c420942ce278e6fed40fa39b01fe1"><strong>paleomix_environment.yaml</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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="17" 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">@@ -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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<td class="new_line diff-line-num" data-linenumber="18" 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">

18

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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>

</pre>

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<td class="new_line diff-line-num" data-linenumber="19" 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="LC19" class="line" lang="yaml">  <span class="pi">-</span> <span class="na" style="color: #008080;">pip</span><span class="pi">:</span></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="20" 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="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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<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">6</span></span></span></pre>

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