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GitLab

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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>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6">f9367bda</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-08-25T16:09:53+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.3.3</pre>

</li>

</ul>

<h4>13 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">

CHANGES.md

</a>

</li>

<li class="file-stats">

<a href="#0fdbda66ca3b7b0b45b2a4108379ad19f7923a9e">

docs/bam_pipeline/configuration.rst

</a>

</li>

<li class="file-stats">

<a href="#e5368178d38862b612c03eac3e417a38b54bc3b6">

docs/bam_pipeline/overview.rst

</a>

</li>

<li class="file-stats">

<a href="#37106ac55933b60ea232abb2c9bb974138d9da0b">

docs/bam_pipeline/requirements.rst

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<li class="file-stats">

<a href="#19d875d2f02769cf6d8972936b903f6bd24332ea">

docs/bam_pipeline/usage.rst

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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

</a>

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<li class="file-stats">

<a href="#ce077518f2a097c8a27352216388e17ae9d5bb9a">

docs/other_tools.rst

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<li class="file-stats">

<a href="#932db922e46b10de6ec4bf49dcb26a3baa73cef8">

docs/yaml.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="#82233c75268e15a595a90e8494933e20039bfa91">

paleomix/nodes/picard.py

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<li class="file-stats">

<a href="#0bb049ed8bfc26bbe651ba505b441330e59eb32e">

paleomix/pipelines/bam/parts/summary.py

</a>

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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/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>

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1

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<td class="new_line diff-line-num" data-linenumber="1" 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">

1

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

<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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<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">

3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.3.3] - 2021-04-06</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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<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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Fixed</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">

6

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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> Fixed regression in BAM pipeline summary node, causing failing if there were zero</span>

</pre>

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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">    hits or reads.</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="8" 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">

8

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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="LC8" class="line" lang="markdown"><span class="p">  -</span> Fixed BAM validation always being run in big-genome mode, resulting in some checks</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">    being disabled despite being applicable.</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">

10

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<pre style="margin: 0;">+<span id="LC10" 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="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="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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## [1.3.2] - 2020-09-03</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="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">

13

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

<pre style="margin: 0;"> <span id="LC13" 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">

5

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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 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="720" 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="729" 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">@@ -720,7 +729,8 @@ the (partially) updated documentation now hosted on ReadTheDocs.</td>

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<td class="old_line diff-line-num" data-linenumber="720" 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">

720

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<td class="new_line diff-line-num" data-linenumber="729" 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">

729

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<pre style="margin: 0;"> <span id="LC729" class="line" lang="markdown"><span class="p">  -</span> Switching to more traditional version-number tracking.</span>

</pre>

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721

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730

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

<pre style="margin: 0;"> <span id="LC730" class="line" lang="markdown"></span>

</pre>

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731

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<pre style="margin: 0;"> <span id="LC731" class="line" lang="markdown"></span>

</pre>

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723

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<td class="new_line diff-line-num old" data-linenumber="732" 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="LC723" 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/v1.3.2...HEAD</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="724" 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="732" 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="LC732" 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/v1.3.3...HEAD</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="724" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="733" 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">

733

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<pre style="margin: 0;">+<span id="LC733" 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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724

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734

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<pre style="margin: 0;"> <span id="LC734" 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>

</pre>

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725

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<td class="new_line diff-line-num" data-linenumber="735" 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="LC735" 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>

</pre>

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726

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<pre style="margin: 0;"> <span id="LC736" class="line" lang="markdown"><span class="p">[</span><span class="ss" style="color: #990073;">1.3.0</span><span class="p">]:</span> <span class="sx" style="color: #d14;">https://github.com/MikkelSchubert/paleomix/compare/v1.2.14...v1.3.0</span></span>

</pre>

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<br>

</li>

<li id="0fdbda66ca3b7b0b45b2a4108379ad19f7923a9e">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#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">@@ -7,15 +7,15 @@ Configuring the BAM pipeline</td>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">The BAM pipeline supports a number of command-line options (see `paleomix bam run --help`). These options may be set directly on the command-line (e.g. using `--max-threads 16`), but it is also possible to set default values for such options.</span>

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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">This is accomplished by writing options in `~/.paleomix/bam_pipeline.ini`::</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">This is accomplished by writing options in `~/.paleomix/bam_pipeline.ini`<span class="idiff left right">, such as</span>::</span>

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11

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

</pre>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">    max-threads = 16</span>

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13

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<td class="new_line diff-line-num old" data-linenumber="13" 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="LC13" class="line" lang="plaintext">    log-level = warning</span>

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14

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<td class="new_line diff-line-num old" data-linenumber="13" 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="LC14" class="line" lang="plaintext">    jar-root = /home/username/install/jar_root</span>

</pre>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">    bowtie2-max-threads = 1</span>

</pre>

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15

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">    bwa-max-threads = 1</span>

</pre>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">    <span class="idiff left">temp</span>-root = /<span class="idiff">tmp</span>/username/<span class="idiff right">bam_pipeline</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">    <span class="idiff left">jar</span>-root = /<span class="idiff">home</span>/username/<span class="idiff right">install/jar_root</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">    jre-option = -Xmx4g</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">    bowtie2-max-threads = 1</span>

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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">    log-level = warning</span>

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">    temp-root = /tmp/username/bam_pipeline</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">Options in the configuration file correspond directly to command-line options for the BAM pipeline, with leading dashes removed. For example, the command-line option `--max-threads` becomes `max-threads` in the configuration file.</span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>

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<br>

</li>

<li id="e5368178d38862b612c03eac3e417a38b54bc3b6">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#e5368178d38862b612c03eac3e417a38b54bc3b6"><strong>docs/bam_pipeline/overview.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">@@ -18,17 +18,17 @@ During a typical analyses, the BAM pipeline will proceed through the following s</td>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">    2. The records of the resulting BAM are updated using `samtools fixmate` to ensure that PE reads contain the correct information about the mate read.</span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">    3. The BAM is sorted using `samtools sort`, indexed using `samtools index`, and validated using <span class="idiff left right">`</span>Picard ValidateSamFile`.</span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">    3. The BAM is sorted using `samtools sort`, indexed using `samtools index`, and validated using Picard <span class="idiff left right">`</span>ValidateSamFile`.</span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">    4. Finally, the records are updated using `samtools calm` to ensure consistent reporting of the number of mismatches relative to the reference genome (BAM tag 'NM').</span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">    4. Finally, the records are updated using `samtools calm<span class="idiff left right">d</span>` to ensure consistent reporting of the number of mismatches relative to the reference genome (BAM tag 'NM').</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">4. Filtering of duplicates, recal<span class="idiff left right">u</span>ation (rescaling) of quality scores, and validation</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">4. Filtering of duplicates, recal<span class="idiff left right">cul</span>ation (rescaling) of quality scores, and validation</span>

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">    1. If enabled, PCR duplicates are filtered using Picard `MarkDuplicates` for SE and PE reads and using `paleomix rmdup_collapsed` for collapsed reads (see the :ref:`other_tools` section). PCR filtering is carried out per library.</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">    2. If mapDamage based rescaling of quality scores is, quality scores of bases that are potentially the result of *post-mortem* DNA damage are recalculated using a damage model built using mapDamage2.0 [Jonsson2013]_.</span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="plaintext">    3. The resulting BAMs are indexed and validated using <span class="idiff left right">`</span>Picard ValidateSamFile`. Mapped reads at each position of the alignments are compared using the query name, sequence, and qualities. If a match is found, it is assumed to represent a duplication of input data (see :ref:`troubleshooting_bam`).</span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">    3. The resulting BAMs are indexed and validated using Picard <span class="idiff left right">`</span>ValidateSamFile`. Mapped reads at each position of the alignments are compared using the query name, sequence, and qualities. If a match is found, it is assumed to represent a duplication of input data (see :ref:`troubleshooting_bam`).</span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">5. Generation of final BAMs</span>

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<pre style="margin: 0;"> <span id="LC34" 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">@@ -38,6 +38,6 @@ During a typical analyses, the BAM pipeline will proceed through the following s</td>

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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext">    1. If the `Summary` feature is enable, a single summary table is generated for each target. This table summarizes the input data in terms of the raw number of reads, the number of reads following filtering / collapsing, the fraction of reads mapped to each prefix, the fraction of reads filtered as duplicates, and more.</span>

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<pre style="margin: 0;"> <span id="LC40" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">    2. Coverage statistics and depth histograms are calculated for the intermediate and final BAM files using `paleomix coverage` and `paleomix depths` if enabled. Statistics are calculated genome-wide and for any regions of interest specified by the user.</span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">    2. Coverage statistics and depth histograms are calculated for the intermediate and final BAM files using `paleomix coverage` and `paleomix depths`<span class="idiff left right">,</span> if enabled. Statistics are calculated genome-wide and for any regions of interest specified by the user.</span>

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<pre style="margin: 0;"> <span id="LC42" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="plaintext">    3. If mapDamage <span class="idiff left right">plotting or modeling </span>is enabled, mapDamage plots are generated; if rescaling is enabled, a model of the post-mortem DNA damage is also generated.</span></pre>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">    3. If mapDamage is enabled, mapDamage plots are generated; if <span class="idiff left right">modeling or </span>rescaling is enabled, a model of the post-mortem DNA damage is also generated.</span></pre>

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<br>

</li>

<li id="37106ac55933b60ea232abb2c9bb974138d9da0b">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#37106ac55933b60ea232abb2c9bb974138d9da0b"><strong>docs/bam_pipeline/requirements.rst</strong></a>

<hr>

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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">@@ -11,12 +11,12 @@ In addition to the requirements listed in the :ref:`installation` section, the B</td>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">* `SAMTools`_ v1.3.1 [Li2009b]_</span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">* `Picard Tools`_ v1.137</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="LC14" class="line" lang="plaintext">The Picard Tools JAR-file (picard.jar) is expected to be located in ~/install/jar_root<span class="idiff left right">/</span> by default, but this behavior may be changed using either the --jar-root command-line option, or via the global configuration file (see section :ref:`bam_configuration`)::</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">The Picard Tools JAR-file (<span class="idiff left">`</span>picard.jar<span class="idiff">`</span>) is expected to be located in <span class="idiff">`</span>~/install/jar_root<span class="idiff">`</span> by default, but this behavior may be changed using either the <span class="idiff">`</span>--jar-root<span class="idiff right">`</span> command-line option, or via the global configuration file (see section :ref:`bam_configuration`)::</span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">    $ mkdir -p ~/install/jar_root</span>

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">    $ wget -O ~/install/jar_root/picard.jar https://github.com/broadinstitute/picard/releases/download/2.23.3/picard.jar</span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">Running Picard requires a Jave Runtime Environment (<span class="idiff left right">JRE</span>). Please refer to your ditro's documentation for how to install a JRE.</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Running Picard requires a Jave Runtime Environment (<span class="idiff left">i.e. the `java` command</span>). Please refer to your di<span class="idiff right">s</span>tro's documentation for how to install a JRE.</span>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">Furthermore, one or both of the following sequence aligners must be installed:</span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">An example project is included with the BAM pipeline, and it is recommended to run this project in order to verify that the pipeline and required applications have been correctly installed. See the :ref:`examples` section for a description of how to run this example project.</span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="plaintext">.. Note::</span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="plaintext">    The example project does not carry out rescaling using mapDamage by default. If you wish to test that the requirements for <span class="idiff left right">this</span> feature have been installed correctly, then change the following line</span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">    The example project does not carry out rescaling using mapDamage by default. If you wish to test that the requirements for <span class="idiff left right">mapDamage rescaling</span> feature have been installed correctly, then change the following line</span>

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

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext">    .. code-block:: yaml</span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext"></span>

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</li>

<li id="19d875d2f02769cf6d8972936b903f6bd24332ea">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#19d875d2f02769cf6d8972936b903f6bd24332ea"><strong>docs/bam_pipeline/usage.rst</strong></a>

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

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">The following describes, step by step, the process of setting up a project for mapping FASTQ reads against a reference sequence using the BAM pipeline. For a detailed description of the configuration file (makefile) used by the BAM pipeline, please refer to the section :ref:`bam_makefile`, and for a detailed description of the files generated by the pipeline, please refer to the section :ref:`bam_filestructure`.</span>

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

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext">The BAM pipeline is invoked using <span class="idiff left">ei</span>the<span class="idiff">r the '</span>paleomix<span class="idiff">'</span> command, which offers access to <span class="idiff">all</span> tools included with PALEOMIX (see section :ref:`other_tools`). For the purpose of these instructions, we will make use of a tiny FASTQ data set included with PALEOMIX pipeline, consisting of synthetic FASTQ reads simulated against the human mitochondrial genome. To follow along, first create a local copy of the <span class="idiff right">BAM pipeline </span>example data:</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">The BAM pipeline is invoked using the<span class="idiff left"> `</span>paleomix<span class="idiff">`</span> command, which offers access to <span class="idiff">the pipelines and to other</span> tools included with PALEOMIX (see section :ref:`other_tools`). For the purpose of these instructions, we will make use of a tiny FASTQ data set included with PALEOMIX pipeline, consisting of synthetic FASTQ reads simulated against the human mitochondrial genome. To follow along, first create a local copy of the example data<span class="idiff right">-set</span>:</span>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">.. code-block:: bash</span>

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

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">    $ paleomix bam example .</span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">This will create a folder named <span class="idiff left">'</span>bam_pipeline<span class="idiff">'</span> in the current folder, which contain the example FASTQ reads and a 'makefile' showcasing various features of the BAM pipeline (<span class="idiff">'</span>makefile.yaml<span class="idiff right">'</span>). We will make use of a subset of the data, but we will not make use of the makefile. The data we will use consists of 3 simulated ancient DNA libraries (independent amplifications), for which either one or two lanes have been simulated:</span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">This will create a folder named <span class="idiff left">`</span>bam_pipeline<span class="idiff">`</span> in the current folder, which contain the example FASTQ reads and a 'makefile' showcasing various features of the BAM pipeline (<span class="idiff">`</span>makefile.yaml<span class="idiff right">`</span>). We will make use of a subset of the data, but we will not make use of the makefile. The data we will use consists of 3 simulated ancient DNA libraries (independent amplifications), for which either one or two lanes have been simulated:</span>

</pre>

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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">+-------------+------+------+-----------------------------+</span>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">| Library     | Lane | Type | Files                       |</span>

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<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_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">

20

</td>

<td class="new_line diff-line-num old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">| ACGATA      |    1 |   PE | data/ACGATA\_L1\_*.fastq.gz |</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="21" 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">

21

</td>

<td class="new_line diff-line-num old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="22" 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">

22

</td>

<td class="new_line diff-line-num old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">| GCTCTG      |    1 |   SE | data/GCTCTG\_L1\_*.fastq.gz |</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

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

23

</td>

<td class="new_line diff-line-num old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

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

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<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

</td>

<td class="new_line diff-line-num old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext">| TGCTCA      |    1 |   SE | data/TGCTCA\_L1\_*.fastq.gz |</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

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

25

</td>

<td class="new_line diff-line-num old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num old" data-linenumber="26" 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">

26

</td>

<td class="new_line diff-line-num old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">|             |    2 |   PE | data/TGCTCA\_L2\_*.fastq.gz |</span>

</pre>

</td>

</tr>

<tr class="line_holder old" id="" style="line-height: 1.6;">

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

27

</td>

<td class="new_line diff-line-num old" data-linenumber="17" 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">

</td>

<td class="line_content old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">

<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="17" 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">

17

</td>

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="18" 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">

18

</td>

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"><span class="idiff left right">  </span>| Library     | Lane | Type | Files                       |</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="19" 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">

19

</td>

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

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="20" 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">

20

</td>

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

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"><span class="idiff left right">  </span>| ACGATA      |    1 |   PE | data/ACGATA\_L1\_*.fastq.gz |</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="21" 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">

21

</td>

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="22" 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">

22

</td>

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"><span class="idiff left right">  </span>| GCTCTG      |    1 |   SE | data/GCTCTG\_L1\_*.fastq.gz |</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

23

</td>

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="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">

24

</td>

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"><span class="idiff left right">  </span>| TGCTCA      |    1 |   SE | data/TGCTCA\_L1\_*.fastq.gz |</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_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">

25

</td>

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="new_line diff-line-num new" data-linenumber="26" 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">

26

</td>

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

<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"><span class="idiff left right">  </span>|             |    2 |   PE | data/TGCTCA\_L2\_*.fastq.gz |</span>

</pre>

</td>

</tr>

<tr class="line_holder new" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num new" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

27

</td>

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

<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<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

</td>

<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">

28

</td>

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

<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

<tr class="line_holder" id="" style="line-height: 1.6;">

<td class="old_line diff-line-num" data-linenumber="29" 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="LC29" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">.. warning::</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">@@ -43,9 +43,9 @@ To start a new project, we must first generate a makefile template using the fol</td>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="plaintext">.. code-block:: bash</span>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext">    $ cd bam_pipeline/</span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="plaintext">    $ paleomix bam m<span class="idiff left right">k</span>file > makefile.yaml</span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">    $ paleomix bam m<span class="idiff left right">ake</span>file > makefile.yaml</span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="plaintext">Once you open the resulting file (<span class="idiff left">'</span>makefile.yaml<span class="idiff">'</span>) in your text editor of choice, you will find that BAM pipeline makefiles are split into <span class="idiff">3</span> major sections, representing 1) the default options<span class="idiff"> used for processing the data</span>; 2) the reference genomes against which reads are to be mapped; and 3) <span class="idiff">sets</span> of input files for <span class="idiff">one or mor</span>e samples which <span class="idiff right">is</span> to be processed.</span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Once you open the resulting file (<span class="idiff left">`</span>makefile.yaml<span class="idiff">`</span>) in your text editor of choice, you will find that BAM pipeline makefiles are split into <span class="idiff">three</span> major sections, representing 1) the default options; 2) the reference genomes against which reads are to be mapped; and 3) <span class="idiff">the</span> of input files for <span class="idiff">th</span>e samples which <span class="idiff right">are</span> to be processed.</span>

</pre>

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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">In a typical project, we will need to review the default options, add one or more reference genomes which we wish to target, and list the input data to be processed.</span>

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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="53" 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="53" 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">@@ -53,44 +53,48 @@ In a typical project, we will need to review the default options, add one or mor</td>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">Default options</span>

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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">^^^^^^^^^^^^^^^</span>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>

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<td class="new_line diff-line-num old" data-linenumber="56" 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="LC56" class="line" lang="plaintext">The makefile starts with an <span class="idiff left">"</span>Options<span class="idiff">"</span> section, which is applied to every set of input-files in the makefile unless explicitly overwritten for a given sample (this is described in the :ref:`bam_makefile` section). For most part, the default values should be suitable for a given project, but special attention should be paid to the following options (<span class="idiff">colons indic</span>ate<span class="idiff right">s</span> subsections):</span>

</pre>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">The makefile starts with an <span class="idiff left">`</span>Options<span class="idiff">`</span> section, which is applied to every set of input-files in the makefile unless explicitly overwritten for a given sample (this is described in the :ref:`bam_makefile` section). For most part, the default values should be suitable for a<span class="idiff">ny</span> given project, but special attention should be paid to the following options (<span class="idiff right">double colons are used to separ</span>ate subsections):</span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="plaintext">**Options\:Platform**</span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">**Options<span class="idiff left"> </span>\:<span class="idiff right">\: </span>Platform**</span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">    The sequencing platform used to generate the sequencing data; this information is recorded in the resulting BAM file, and may be used by downstream tools. The `SAM/BAM specification`_ the valid platforms, which currently include <span class="idiff left">'</span>CAPILLARY<span class="idiff">'</span>, <span class="idiff">'</span>HELICOS<span class="idiff">'</span>, <span class="idiff">'</span>ILLUMINA<span class="idiff">'</span>, <span class="idiff">'</span>IONTORRENT<span class="idiff">'</span>, <span class="idiff">'</span>LS454<span class="idiff">'</span>, <span class="idiff">'</span>ONT<span class="idiff">'</span>, <span class="idiff">'</span>PACBIO<span class="idiff">'</span>, and <span class="idiff">'</span>SOLID<span class="idiff right">'</span>.</span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">    The sequencing platform used to generate the sequencing data; this information is recorded in the resulting BAM file, and may be used by downstream tools. The `SAM/BAM specification`_ the valid platforms, which currently include <span class="idiff left">`</span>CAPILLARY<span class="idiff">`</span>, <span class="idiff">`</span>HELICOS<span class="idiff">`</span>, <span class="idiff">`</span>ILLUMINA<span class="idiff">`</span>, <span class="idiff">`</span>IONTORRENT<span class="idiff">`</span>, <span class="idiff">`</span>LS454<span class="idiff">`</span>, <span class="idiff">`</span>ONT<span class="idiff">`</span>, <span class="idiff">`</span>PACBIO<span class="idiff">`</span>, and <span class="idiff">`</span>SOLID<span class="idiff right">`</span>.</span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">**Options\:QualityOffset**</span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">**Options<span class="idiff left"> </span>\:<span class="idiff right">\: </span>QualityOffset**</span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="plaintext">    The QualityOffset option refers to the starting ASCII value used to encode `Phred quality-scores`_ in user-provided FASTQ files, with the possible values of 33, 64, and <span class="idiff left">'</span>Solexa<span class="idiff">'</span>. For most modern data, this will be 33, corresponding to ASCII characters in the range <span class="idiff">'!'</span> to <span class="idiff">'J'</span>. Older data is often encoded using the offset 64, corresponding to ASCII characters in the range <span class="idiff">'@'</span> to <span class="idiff">'h'</span>, and more rarely using Solexa quality-scores, which represent a different scheme than Phred scores, and which occupy the range of ASCII values from <span class="idiff">';'</span> to <span class="idiff">'h'</span>. For a visual representation of this, refer to the <span class="idiff right">Wikipedia article linked abov</span>e.</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">    The QualityOffset option refers to the starting ASCII value used to encode `Phred quality-scores`_ in user-provided FASTQ files, with the possible values of 33, 64, and <span class="idiff left">`</span>Solexa<span class="idiff">`</span>. For most modern data, this will be 33, corresponding to ASCII characters in the range <span class="idiff">`!`</span> to <span class="idiff">`J`</span>. Older data is often encoded using the offset 64, corresponding to ASCII characters in the range <span class="idiff">`@`</span> to <span class="idiff">`h`</span>, and more rarely using Solexa quality-scores, which represent a different scheme than Phred scores, and which occupy the range of ASCII values from <span class="idiff">`;`</span> to <span class="idiff">`h`</span>. For a visual representation of this, refer to the <span class="idiff right">`Phred quality-scores`_ pag</span>e.</span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="plaintext">.. warning::</span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="plaintext">    By default, the adapter trimming software used by PALEOMIX expects quality-scores no <span class="idiff left">high</span>er than 41, corresponding to the ASCII character <span class="idiff">'J'</span> when encoded using offset 33. If the input-data contains quality-scores higher greater than this value, then it is necessary to specify the maximum value using the <span class="idiff">'</span>--qualitymax<span class="idiff right">'</span> command-line option. See below.</span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">    By default, the adapter trimming software used by PALEOMIX expects quality-scores no <span class="idiff left">great</span>er than 41, corresponding to the ASCII character <span class="idiff">`J`</span> when encoded using offset 33. If the input-data contains quality-scores higher greater than this value, then it is necessary to specify the maximum value using the <span class="idiff">`</span>--qualitymax<span class="idiff right">`</span> command-line option. See below.</span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext">.. warning::</span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="plaintext">    Presently, quality-offsets other than 33 are not supported when using the BWA <span class="idiff left">'</span>mem<span class="idiff">'</span> or the BWA <span class="idiff">'</span>bwasw<span class="idiff right">'</span> algorithms. To use these algorithms with quality-offset 64 data, it is therefore necessary to first convert these data to offset 33. This can be accomplished using the `seqtk`_ tool.</span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">    Presently, quality-offsets other than 33 are not supported when using the BWA <span class="idiff left">`</span>mem<span class="idiff">`</span> or the BWA <span class="idiff">`</span>bwasw<span class="idiff right">`</span> algorithms. To use these algorithms with quality-offset 64 data, it is therefore necessary to first convert these data to offset 33. This can be accomplished using the `seqtk`_ tool.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="plaintext">**Options\:AdapterRemoval\:--adapter1**</span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">**Options\:AdapterRemoval\:--adapter2**</span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">**Options \:\: AdapterRemoval \:\: --adapter1** and **Options \:\: AdapterRemoval \:\: --adapter2**</span>

</pre>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">These two options are used to specify the adapter sequences used to identify and trim reads that contain adapter contamination using AdapterRemoval. Thus, the sequence provided for --adapter1 is expected to be found in the mate 1 reads, and the sequence specified for --adapter2 is expected to be found in the mate 2 reads. In both cases, these should be specified as in the orientation that appear in these files (i.e. it should be possible to grep the files for these, assuming that the reads were long enough, <span class="idiff left">and</span> treat<span class="idiff">ing</span> Ns as wildcards).<span class="idiff right"> It is very important that these be specified correctly. Please refer to the `AdapterRemoval documentation`_ for more information.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">These two options are used to specify the adapter sequences used to identify and trim reads that contain adapter contamination using AdapterRemoval. Thus, the sequence provided for <span class="idiff left">`</span>--adapter1<span class="idiff">`</span> is expected to be found in the mate 1 reads, and the sequence specified for <span class="idiff">`</span>--adapter2<span class="idiff">`</span> is expected to be found in the mate 2 reads. In both cases, these should be specified as in the orientation that appear in these files (i.e. it should be possible to grep the files for these<span class="idiff"> sequences</span>, assuming that the reads were long enough, <span class="idiff right">if you</span> treat Ns as wildcards).</span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="plaintext">**Aligners\:Program**</span>

</pre>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">.. warning::</span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">  It is very important that the correct adapter sequences are used. Please refer to the `AdapterRemoval documentation`_ for more information and for help identifying the adapters for paired-end reads.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">**Aligners \:\: Program**</span>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC82" class="line" lang="plaintext">    The short read alignment program to use to map the (trimmed) reads to the reference genome. Currently, users many choose between <span class="idiff left">'</span>BWA<span class="idiff">'</span> and <span class="idiff">'</span>Bowtie2<span class="idiff right">'</span>, with additional options available for each program.</span>

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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">    The short read alignment program to use to map the (trimmed) reads to the reference genome. Currently, users many choose between <span class="idiff left">`</span>BWA<span class="idiff">`</span> and <span class="idiff">`</span>Bowtie2<span class="idiff right">`</span>, with additional options available for each program.</span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="plaintext">**Aligners\:<span class="idiff left right">BWA\:MinQuality** and **Aligners\:Bowtie2</span>\:MinQuality**</span>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">**Aligners<span class="idiff left"> </span>\:<span class="idiff">\: \* \:</span>\:<span class="idiff right"> </span>MinQuality**</span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext">    The minimum mapping quality of hits to retain during the mapping process. If this option is set to a non-zero value, any hits with a mapping quality below this value are removed from the resulting BAM file (this option does not apply to unmapped reads). If the final BAM should contain all reads in the input files, this option must be set to 0, and the <span class="idiff left">'</span>FilterUnmappedReads<span class="idiff">'</span> option set to <span class="idiff">'</span>no<span class="idiff right">'</span>.</span>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">    The minimum mapping quality of hits to retain during the mapping process. If this option is set to a non-zero value, any hits with a mapping quality below this value are removed from the resulting BAM file (this option does not apply to unmapped reads). If the final BAM should contain all reads in the input files, this option must be set to 0, and the <span class="idiff left">`</span>FilterUnmappedReads<span class="idiff">`</span> option set to <span class="idiff">`</span>no<span class="idiff right">`</span>.</span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="plaintext">**Aligners\:BWA\:UseSeed**</span>

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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">**Aligners<span class="idiff left"> </span>\:<span class="idiff">\: </span>BWA<span class="idiff"> </span>\:<span class="idiff right">\: </span>UseSeed**</span>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="plaintext">    Enable/disable the use of a seed region when mapping reads using the BWA <span class="idiff left">'</span>backtrack<span class="idiff right">'</span> alignment algorithm (the default). Disabling this option may yield some improvements in the alignment of highly damaged ancient DNA, at the cost of significantly increasing the running time. As such, this option is not recommended for modern samples [Schubert2012]_.</span>

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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">    Enable/disable the use of a seed region when mapping reads using the BWA <span class="idiff left">`</span>backtrack<span class="idiff right">`</span> alignment algorithm (the default). Disabling this option may yield some improvements in the alignment of highly damaged ancient DNA, at the cost of significantly increasing the running time. As such, this option is not recommended for modern samples [Schubert2012]_.</span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">For the purpose of the example project, we need only change a few options. Since the reads were simulated using an Phred score offset of 33, there is no need to change the <span class="idiff left">'</span>QualityOffset<span class="idiff">'</span> option, and since the simulated adapter sequences matches the adapters that AdapterRemoval searches for by default, so we do not need to set eiter of <span class="idiff">'</span>--adapter1<span class="idiff">'</span> or <span class="idiff">'</span>--adapter2<span class="idiff">'</span>. We will, however, use the default mapping program (BWA) and algorithm (<span class="idiff">'</span>backtrack<span class="idiff">'</span>), but change the minimum mapping quality to 30 (corresponding to an error probability of 0.001). Changing the minimum quality is accomplished by locating the <span class="idiff">'</span>Aligners<span class="idiff">'</span> section of the makefile, and changing the <span class="idiff">'</span>MinQuality<span class="idiff">'</span> value from 0 to 30 (line <span class="idiff right">12</span>):</span>

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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">For the purpose of the example project, we need only change a few options. Since the reads were simulated using an Phred score offset of 33, there is no need to change the <span class="idiff left">`</span>QualityOffset<span class="idiff">`</span> option, and since the simulated adapter sequences matches the adapters that AdapterRemoval searches for by default, so we do not need to set eit<span class="idiff">h</span>er of <span class="idiff">`</span>--adapter1<span class="idiff">`</span> or <span class="idiff">`</span>--adapter2<span class="idiff">`</span>. We will, however, use the default mapping program (BWA) and algorithm (<span class="idiff">`</span>backtrack<span class="idiff">`</span>), but change the minimum mapping quality to 30 (corresponding to an error probability of 0.001). Changing the minimum quality is accomplished by locating the <span class="idiff">`</span>Aligners<span class="idiff">`</span> section of the makefile, and changing the <span class="idiff">`</span>MinQuality<span class="idiff">`</span> value from 0 to 30 (line <span class="idiff right">40</span>):</span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">.. code-block:: yaml</span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext">    :emphasize-lines: 12</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">@@ -116,7 +120,7 @@ For the purpose of the example project, we need only change a few options. Since</td>

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<pre style="margin: 0;"> <span id="LC120" class="line" lang="plaintext">        # have few errors (sets "-l"). See http://pmid.us/22574660</span>

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<pre style="margin: 0;"> <span id="LC121" class="line" lang="plaintext">        UseSeed: yes</span>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC119" class="line" lang="plaintext">Since the data we will be mapping represents (simulated) ancient DNA, we will furthermore set the UseSeed option to <span class="idiff left">'</span>no<span class="idiff">'</span> (line <span class="idiff">18</span>), in order to recover a small additional amount of alignments during mapping (<span class="idiff right">c.f.</span> [Schubert2012]_):</span>

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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">Since the data we will be mapping represents (simulated) ancient DNA, we will furthermore set the UseSeed option to <span class="idiff left">`</span>no<span class="idiff">`</span> (line <span class="idiff">55</span>), in order to recover a small additional amount of alignments during mapping (<span class="idiff right">see</span> [Schubert2012]_):</span>

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<pre style="margin: 0;"> <span id="LC124" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC125" class="line" lang="plaintext">.. code-block:: yaml</span>

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="plaintext">    :emphasize-lines: 18</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="148" 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">@@ -148,24 +152,24 @@ Once this is done, we can proceed to specify the location of the reference genom</td>

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<pre style="margin: 0;"> <span id="LC152" class="line" lang="plaintext">Reference genomes (prefixes)</span>

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<pre style="margin: 0;"> <span id="LC153" class="line" lang="plaintext">----------------------------</span>

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

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<td class="new_line diff-line-num old" data-linenumber="155" 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="LC151" class="line" lang="plaintext">Mapping is carried out using one or more reference genomes (or other sequences) in the form of FASTA files, which are indexed for use in read mapping (automatically, by the pipeline) using either the <span class="idiff left">"</span>bwa index<span class="idiff">"</span> or <span class="idiff">"</span>bowtie2-build<span class="idiff right">"</span> commands. Since sequence alignment index are generated at the location of these files, reference genomes are also referred to as "prefixes" in the documentation. In other words, using BWA as an example, the PALEOMIX pipeline will generate a index (prefix) of the reference genome using a command corresponding to the following, for BWA:</span>

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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">Mapping is carried out using one or more reference genomes (or other sequences) in the form of FASTA files, which are indexed for use in read mapping (automatically, by the pipeline) using either the <span class="idiff left">`</span>bwa index<span class="idiff">`</span> or <span class="idiff">`</span>bowtie2-build<span class="idiff right">`</span> commands. Since sequence alignment index are generated at the location of these files, reference genomes are also referred to as "prefixes" in the documentation. In other words, using BWA as an example, the PALEOMIX pipeline will generate a index (prefix) of the reference genome using a command corresponding to the following, for BWA:</span>

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<pre style="margin: 0;"> <span id="LC156" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="153" 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="LC157" class="line" lang="plaintext">.. code-block:: bash</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="154" 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="LC158" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="155" 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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<td class="new_line diff-line-num old" data-linenumber="159" 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="LC155" class="line" lang="plaintext">    $ bwa index prefixes/my_genome.fa</span>

</pre>

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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">    $ bwa index prefixes/my_genome.fa<span class="idiff left right">sta</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC160" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="161" 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="LC157" class="line" lang="plaintext">In addition to the BWA / Bowtie2 index, several other related files are also automatically generated, including a FASTA index file (.fai), which are required for various operations of the pipeline. These are similarly located at the same folder as the reference FASTA file. For a more detailed description, please refer to the :ref:`bam_filestructure` section.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">In addition to the BWA / Bowtie2 index, several other related files are also automatically generated, including a FASTA index file (<span class="idiff left">`</span>.fai<span class="idiff right">`</span>), which are required for various operations of the pipeline. These are similarly located at the same folder as the reference FASTA file. For a more detailed description, please refer to the :ref:`bam_filestructure` section.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC163" class="line" lang="plaintext">.. warning::</span>

</pre>

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<pre style="margin: 0;"> <span id="LC164" class="line" lang="plaintext">    Since the pipeline automatically carries out indexing of the FASTA files, it therefore requires write-access to the folder containing the FASTA files. If this is not possible, one may simply create a local folder containing symbolic links to the original FASTA file(s), and point the makefile to this location. All automatically generated files will then be placed in this location.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC165" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="166" 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="LC162" class="line" lang="plaintext">Specifying which FASTA file to align sequences is accomplished by listing these in the <span class="idiff left">"</span>Prefixes<span class="idiff">"</span> section in the makefile. For example, assuming that we had a FASTA file named <span class="idiff">"</span>my\_genome.fasta<span class="idiff">"</span> which is located in the <span class="idiff">folder "</span>my\_prefixes<span class="idiff right">"</span>, the following might be used::</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="166" 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="LC166" class="line" lang="plaintext">Specifying which FASTA file to align sequences is accomplished by listing these in the <span class="idiff left">`</span>Prefixes<span class="idiff">`</span> section in the makefile. For example, assuming that we had a FASTA file named <span class="idiff">`</span>my\_genome.fasta<span class="idiff">`</span> which is located in the <span class="idiff">`</span>my\_prefixes<span class="idiff right">` folder</span>, the following might be used::</span>

</pre>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC168" class="line" lang="plaintext">    Prefixes:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC169" class="line" lang="plaintext">      my_genome:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC170" class="line" lang="plaintext">        Path: my_prefixes/my_genome.fasta</span>

</pre>

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<pre style="margin: 0;"> <span id="LC171" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC168" class="line" lang="plaintext">The name of the prefix (here <span class="idiff left">'</span>my\_genome<span class="idiff">'</span>) will be used to name the resulting files and in various tables that are generated by the pipeline. Typical names include <span class="idiff">'</span>hg19<span class="idiff">'</span>, <span class="idiff">'</span>EquCab20<span class="idiff right">'</span>, and other standard abbreviations for reference genomes, accession numbers, and the like. Multiple prefixes can be specified, but each name MUST be unique::</span>

</pre>

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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">The name of the prefix (here <span class="idiff left">`</span>my\_genome<span class="idiff">`</span>) will be used to name the resulting files and in various tables that are generated by the pipeline. Typical names include <span class="idiff">`</span>hg19<span class="idiff">`</span>, <span class="idiff">`</span>EquCab20<span class="idiff right">`</span>, and other standard abbreviations for reference genomes, accession numbers, and the like. Multiple prefixes can be specified, but each name MUST be unique::</span>

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<pre style="margin: 0;"> <span id="LC173" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC174" class="line" lang="plaintext">    Prefixes:</span>

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<pre style="margin: 0;"> <span id="LC175" class="line" lang="plaintext">      my_genome:</span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="177" 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">@@ -173,7 +177,7 @@ The name of the prefix (here 'my\_genome') will be used to name the resulting fi</td>

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<pre style="margin: 0;"> <span id="LC177" class="line" lang="plaintext">      my_other_genome:</span>

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="plaintext">        Path: my_prefixes/my_other_genome.fasta</span>

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="plaintext">In the case of this example project, we will be mapping our data against the revised Cambridge Reference Sequence (rCRS) for the human mitochondrial genome, which is included in examples folder under <span class="idiff left">'</span>prefixes<span class="idiff">'</span>, as a file named <span class="idiff">'</span>rCRS.fasta<span class="idiff">'</span>. To add it to the makefile, locate the <span class="idiff">'</span>Prefixes<span class="idiff">'</span> section located below the <span class="idiff">'</span>Options<span class="idiff">'</span> section, and update it as described above (lines 5 and <span class="idiff right">7</span>):</span>

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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">In the case of this example project, we will be mapping our data against the revised Cambridge Reference Sequence (rCRS) for the human mitochondrial genome, which is included in examples folder under <span class="idiff left">`</span>prefixes<span class="idiff">`</span>, as a file named <span class="idiff">`</span>rCRS.fasta<span class="idiff">`</span>. To add it to the makefile, locate the <span class="idiff">`</span>Prefixes<span class="idiff">`</span> section located below the <span class="idiff">`</span>Options<span class="idiff">`</span> section, and update it as described above (lines <span class="idiff">11</span>5 and <span class="idiff right">119</span>):</span>

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC182" class="line" lang="plaintext">.. code-block:: yaml</span>

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext">    :emphasize-lines: 6,10</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="191" 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="195" 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">@@ -191,13 +195,13 @@ In the case of this example project, we will be mapping our data against the rev</td>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="plaintext">        # recommended (e.g. /path/to/Human_g1k_v37.fasta should be named 'Human_g1k_v37').</span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="plaintext">        Path: prefixes/rCRS.fasta</span>

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<td class="new_line diff-line-num" data-linenumber="197" 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="LC197" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="plaintext">Once this is done, we may specify the input data that we w<span class="idiff left">ish</span> the pipeline to process<span class="idiff right"> for us</span>.</span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">Once this is done, we may specify the input data that we w<span class="idiff left right">ant</span> the pipeline to process.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC199" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC200" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC201" class="line" lang="plaintext">Specifying read data</span>

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<pre style="margin: 0;"> <span id="LC202" class="line" lang="plaintext">--------------------</span>

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<pre style="margin: 0;"> <span id="LC203" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC200" class="line" lang="plaintext">A single makefile may be used to process one or more samples, to generate one or more BAM files and supplementary statistics. In this project we will only deal with a single sample, which we accomplish by adding creating our own section at the end of the makefile. The first step is to determine the name for the files generated by the BAM pipeline. Specifically, we will specify a name which is prefixed to all output generated for our sample (here named <span class="idiff left">'</span>MyFilename<span class="idiff right">'</span>), by adding the following line to the end of the makefile:</span>

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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">A single makefile may be used to process one or more samples, to generate one or more BAM files and supplementary statistics. In this project we will only deal with a single sample, which we accomplish by adding creating our own section at the end of the makefile. The first step is to determine the name for the files generated by the BAM pipeline. Specifically, we will specify a name which is prefixed to all output generated for our sample (here named <span class="idiff left">`</span>MyFilename<span class="idiff right">`</span>), by adding the following line to the end of the makefile:</span>

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<pre style="margin: 0;"> <span id="LC205" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC206" class="line" lang="plaintext">.. code-block:: yaml</span>

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<pre style="margin: 0;"> <span id="LC207" class="line" lang="plaintext">    :linenos:</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">@@ -217,21 +221,21 @@ This first name, or grouping, is referred to as the target, and typically corres</td>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="plaintext">    MyFilename:</span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="plaintext">      MySample:</span>

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<pre style="margin: 0;"> <span id="LC223" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC220" class="line" lang="plaintext">Similarly, we need to specify the name of each library in our dataset. By convention, I often use the index used to construct the library as the library name (which allows for easy identification), but any name may be used for a library, provided that it unique to that sample. As described near the start of this document, we are dealing with 3 libraries:</span>

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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">Similarly, we need to specify the name of each library in our data<span class="idiff left right"> </span>set. By convention, I often use the index used to construct the library as the library name (which allows for easy identification), but any name may be used for a library, provided that it unique to that sample. As described near the start of this document, we are dealing with 3 libraries:</span>

</pre>

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<pre style="margin: 0;"> <span id="LC225" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC222" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

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<pre style="margin: 0;">-<span id="LC223" class="line" lang="plaintext">| Library     | Lane | Type | Fi<span class="idiff left right">e</span>ls                       |</span>

</pre>

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<pre style="margin: 0;">-<span id="LC224" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

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<pre style="margin: 0;">-<span id="LC225" class="line" lang="plaintext">| ACGATA      |    1 |   PE | data/ACGATA\_L1\_*.fastq.gz |</span>

</pre>

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<pre style="margin: 0;">-<span id="LC226" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="226" 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="LC227" class="line" lang="plaintext">| GCTCTG      |    1 |   SE | data/GCTCTG\_L1\_*.fastq.gz |</span>

</pre>

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<pre style="margin: 0;">-<span id="LC228" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

</pre>

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<pre style="margin: 0;">-<span id="LC229" class="line" lang="plaintext">| TGCTCA      |    1 |   SE | data/TGCTCA\_L1\_*.fastq.gz |</span>

</pre>

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<pre style="margin: 0;">-<span id="LC230" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

</pre>

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<pre style="margin: 0;">-<span id="LC231" class="line" lang="plaintext">|             |    2 |   PE | data/TGCTCA\_L2\_*.fastq.gz |</span>

</pre>

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<pre style="margin: 0;">-<span id="LC232" class="line" lang="plaintext">+-------------+------+------+-----------------------------+</span>

</pre>

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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"><span class="idiff left">  </span>| Library     | Lane | Type | Fil<span class="idiff right">e</span>s                       |</span>

</pre>

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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"><span class="idiff left right">  </span>| ACGATA      |    1 |   PE | data/ACGATA\_L1\_*.fastq.gz |</span>

</pre>

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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="231" 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="LC231" class="line" lang="plaintext"><span class="idiff left right">  </span>| GCTCTG      |    1 |   SE | data/GCTCTG\_L1\_*.fastq.gz |</span>

</pre>

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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"><span class="idiff left right">  </span>| TGCTCA      |    1 |   SE | data/TGCTCA\_L1\_*.fastq.gz |</span>

</pre>

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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"><span class="idiff left right">  </span>|             |    2 |   PE | data/TGCTCA\_L2\_*.fastq.gz |</span>

</pre>

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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"><span class="idiff left right">  </span>+-------------+------+------+-----------------------------+</span>

</pre>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="238" 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="LC234" class="line" lang="plaintext">It is important to correctly specify the libraries, since the pipeline will not only use this information for summary statistics and record it in the resulting BAM files, but will also carry out filtering of PCR duplicates (and other analyses) on a per-library basis. Wrongly grouping together data will therefore result in a loss of useful alignments wrongly identified as PCR duplicates, or, similarly, in the inclusion of reads that should have been filtered as PCR duplicates. The library names are added below the name of the sample (<span class="idiff left">'</span>MySample<span class="idiff right">'</span>), in a similar manner to the sample itself:</span>

</pre>

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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">It is important to correctly specify the libraries, since the pipeline will not only use this information for summary statistics and record it in the resulting BAM files, but will also carry out filtering of PCR duplicates (and other analyses) on a per-library basis. Wrongly grouping together data will therefore result in a loss of useful alignments wrongly identified as PCR duplicates, or, similarly, in the inclusion of reads that should have been filtered as PCR duplicates. The library names are added below the name of the sample (<span class="idiff left">`</span>MySample<span class="idiff right">`</span>), in a similar manner to the sample itself:</span>

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<pre style="margin: 0;"> <span id="LC239" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="plaintext">.. code-block:: yaml</span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="plaintext">    :linenos:</span>

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<pre style="margin: 0;"> <span id="LC250" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC251" class="line" lang="plaintext">        TGCTCA:</span>

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<pre style="margin: 0;"> <span id="LC252" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC249" class="line" lang="plaintext">The final step involves specifying the location of the raw FASTQ reads that should be processed for each library, and consists of specifying one or more "lanes" of reads, each of which must be given a unique name. For single-end reads, this is accomplished simply by providing a path (with optional wildcards) to the location of the file(s). For example, for lane 1 of library ACGATA, the files are located at data/ACGATA\_L1\_*.fastq.gz:</span>

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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">The final step involves specifying the location of the raw FASTQ reads that should be processed for each library, and consists of specifying one or more "lanes" of reads, each of which must be given a unique name. For single-end reads, this is accomplished simply by providing a path (with optional wildcards) to the location of the file(s). For example, for lane 1 of library ACGATA, the files are located at <span class="idiff left">`</span>data/ACGATA\_L1\_*.fastq.gz<span class="idiff right">`</span>:</span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="plaintext">.. code-block:: bash</span>

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<pre style="margin: 0;"> <span id="LC256" 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">@@ -286,7 +290,7 @@ Specifying the location of paired-end data is slightly more complex, since the p</td>

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<pre style="margin: 0;"> <span id="LC290" class="line" lang="plaintext">    data/ACGATA_L1_R2_03.fastq.gz</span>

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<pre style="margin: 0;"> <span id="LC291" class="line" lang="plaintext">    data/ACGATA_L1_R2_04.fastq.gz</span>

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<pre style="margin: 0;"> <span id="LC292" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC289" class="line" lang="plaintext">Knowing how that the files contain a number specifying which file in a pair they correspond to, we can then construct a path that includes the keyword <span class="idiff left">'</span>{Pair}<span class="idiff">'</span> in place of that number. For the above example, that path would therefore be <span class="idiff">'</span>data/ACGATA\_L1\_R{Pair}_*.fastq.gz<span class="idiff">'</span> (corresponding to <span class="idiff">'</span>data/ACGATA\_L1\_R[12]_*.fastq.gz<span class="idiff right">'</span>):</span>

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">Knowing how that the files contain a number specifying which file in a pair they correspond to, we can then construct a path that includes the keyword <span class="idiff left">`</span>{Pair}<span class="idiff">`</span> in place of that number. For the above example, that path would therefore be <span class="idiff">`</span>data/ACGATA\_L1\_R{Pair}_*.fastq.gz<span class="idiff">`</span> (corresponding to <span class="idiff">`</span>data/ACGATA\_L1\_R[12]_*.fastq.gz<span class="idiff right">`</span>):</span>

</pre>

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<pre style="margin: 0;"> <span id="LC294" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC295" class="line" lang="plaintext">.. code-block:: yaml</span>

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<pre style="margin: 0;"> <span id="LC296" class="line" lang="plaintext">    :linenos:</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">@@ -469,7 +473,7 @@ With this makefile in hand, the pipeline may be executed using the following com</td>

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<pre style="margin: 0;"> <span id="LC473" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC474" class="line" lang="plaintext">    $ paleomix bam run makefile.yaml</span>

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<pre style="margin: 0;"> <span id="LC475" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC472" class="line" lang="plaintext">The pipeline will run as many simultaneous processes as there are cores in the current system, but this behavior may be changed by using the <span class="idiff left">'</span>--max-threads<span class="idiff">'</span> command-line option. Use the <span class="idiff">'</span>--help<span class="idiff">'</span> command-line option to view additional options available when running the pipeline. By default, output files are placed in the same folder as the makefile, but this behavior may be changed by setting the <span class="idiff">'</span>--destination<span class="idiff right">'</span> command-line option. For this projects, these files include the following:</span>

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<pre style="margin: 0;">+<span id="LC476" class="line" lang="plaintext">The pipeline will run as many simultaneous processes as there are cores in the current system, but this behavior may be changed by using the <span class="idiff left">`</span>--max-threads<span class="idiff">`</span> command-line option. Use the <span class="idiff">`</span>--help<span class="idiff">`</span> command-line option to view additional options available when running the pipeline. By default, output files are placed in the same folder as the makefile, but this behavior may be changed by setting the <span class="idiff">`</span>--destination<span class="idiff right">`</span> command-line option. For this projects, these files include the following:</span>

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<td class="new_line diff-line-num" data-linenumber="477" 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="LC477" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC478" class="line" lang="plaintext">.. code-block:: bash</span>

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<pre style="margin: 0;"> <span id="LC479" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="480" 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="484" 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">@@ -480,10 +484,10 @@ The pipeline will run as many simultaneous processes as there are cores in the c</td>

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<pre style="margin: 0;"> <span id="LC484" class="line" lang="plaintext">    MyFilename.rCRS.mapDamage</span>

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<td class="new_line diff-line-num" data-linenumber="485" 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="LC485" class="line" lang="plaintext">    MyFilename.summary</span>

</pre>

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<pre style="margin: 0;"> <span id="LC486" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="487" 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="LC483" class="line" lang="plaintext">The files include a table of the average coverage, a histogram of the per-site coverage (depths), a folder containing one set of mapDamage plots per library, and the final BAM file and its index (the .bai file), as well as a table summarizing the entire analysis. For a more detailed description of the files generated by the pipeline, please refer to the :ref:`bam_filestructure` section; should problems occur during the execution of the pipeline, then please verify that the makefile is correctly filled out as described above, and refer to the :ref:`troubleshooting_bam` section.</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="487" 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="LC487" class="line" lang="plaintext">The files include a table of the average coverage, a histogram of the per-site coverage (depths), a folder containing one set of mapDamage plots per library, and the final BAM file and its index (the <span class="idiff left">`</span>.bai<span class="idiff right">`</span> file), as well as a table summarizing the entire analysis. For a more detailed description of the files generated by the pipeline, please refer to the :ref:`bam_filestructure` section; should problems occur during the execution of the pipeline, then please verify that the makefile is correctly filled out as described above, and refer to the :ref:`troubleshooting_bam` section.</span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="488" 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="LC488" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC489" class="line" lang="plaintext">.. note::</span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="490" 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="LC486" class="line" lang="plaintext">    The first item, <span class="idiff left">'</span>MyFilename<span class="idiff right">'</span>, is a folder containing intermediate files generated while running the pipeline, required due to the many steps involved in a typical analyses, and which also allows for the pipeline to resume should the process be interrupted. This folder will typically take up 3-4x the disk-space used by the final BAM file(s), and can safely be removed once the pipeline has run to completion, in order to reduce disk-usage.</span>

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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext">    The first item, <span class="idiff left">`</span>MyFilename<span class="idiff right">`</span>, is a folder containing intermediate files generated while running the pipeline, required due to the many steps involved in a typical analyses, and which also allows for the pipeline to resume should the process be interrupted. This folder will typically take up 3-4x the disk-space used by the final BAM file(s), and can safely be removed once the pipeline has run to completion, in order to reduce disk-usage.</span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC493" class="line" lang="plaintext">.. _SAM/BAM specification: http://samtools.sourceforge.net/SAM1.pdf</span>

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<li id="254a2da7a740675e537439eb88e32083b9ea4771">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#254a2da7a740675e537439eb88e32083b9ea4771"><strong>docs/conf.py</strong></a>

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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">2</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">3</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/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#5f751d21bc12129082e8f5d7b3edbc140a238ce7"><strong>docs/installation.rst</strong></a>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">The following instructions will install PALEOMIX for the current user, but does not include specific programs required by the pipelines. For pipeline specific instructions, refer to the requirements sections for the :ref:`BAM <bam_requirements>`, the :ref:`Phylogentic <phylo_requirements>`, and the :ref:`Zonkey <zonkey_requirements>` pipeline.</span>

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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">The recommended way of installing PALEOMIX is by use of the `pip`_ package manager for Python 3. If <span class="idiff left">`</span>pip<span class="idiff">`</span> is not installed, then please consult the documentation for your operating system. For Debian based operating systems, <span class="idiff">`</span>pip<span class="idiff right">`</span> may be installed as follows::</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">The recommended way of installing PALEOMIX is by use of the `pip`_ package manager for Python 3. If pip is not installed, then please consult the documentation for your operating system. For Debian based operating systems, pip may be installed as follows::</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">    $ sudo apt-get install python3-pip</span>

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<pre style="margin: 0;"> <span id="LC13" 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">@@ -51,16 +51,14 @@ Once `venv` is installed, creation of a virtual environment and installation of</td>

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

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<pre style="margin: 0;"> <span id="LC52" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC53" class="line" lang="plaintext">    $ python3 -m venv venv</span>

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<td class="new_line diff-line-num old" data-linenumber="54" 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="LC54" class="line" lang="plaintext">    $ source ./venv/bin/activate</span>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="plaintext">    $ (venv) pip install paleomix==\ |release|</span>

</pre>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="plaintext">    $ (venv) deactivate</span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">    $ ./venv/bin/pip install paleomix==\ |release|</span>

</pre>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="56" 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="LC58" class="line" lang="plaintext">Following successful completion of these commands, the <span class="idiff left">PALEOMIX tools</span> 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` <span class="idiff right">commands</span> to a folder in your `PATH`. This can be accomplished as follows::</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="56" 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="LC56" class="line" lang="plaintext">Following successful completion of these commands, the <span class="idiff left">`paleomix` executable</span> 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` <span class="idiff right">executable</span> to a folder in your `PATH`. This can be accomplished as follows::</span>

</pre>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext">    $ mkdir -p ~/.local/bin/</span>

</pre>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">    $ ln -s ${PWD}/venv/bin/paleomix ~/.local/bin/</span>

</pre>

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="plaintext"></span>

</pre>

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<td class="new_line diff-line-num old" data-linenumber="61" 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="LC63" class="line" lang="plaintext">If ~/.local/bin is not already in your PATH, then it can be added as follows:</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="64" 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="LC61" class="line" lang="plaintext">If ~/.local/bin is not already in your PATH, then it can be added as follows:<span class="idiff left right">:</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">    $ echo 'export PATH=~/.local/bin:$PATH' >> ~/.bashrc</span>

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<pre style="margin: 0;"> <span id="LC64" 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">@@ -72,15 +70,13 @@ Upgrade an existing installation of PALEOMIX, installed using the methods descri</td>

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<pre style="margin: 0;"> <span id="LC70" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">    $ pip install --upgrade paleomix</span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="plaintext">To upgrade an installation a self-contained installation, <span class="idiff left">activate</span> th<span class="idiff">e</span> environment<span class="idiff right"> before calling `pip`</span>::</span>

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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">To upgrade an installation a self-contained installation, <span class="idiff left">simply call the `pip` executable in</span> th<span class="idiff right">at</span> environment::</span>

</pre>

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<pre style="margin: 0;"> <span id="LC74" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="plaintext">    $ source ./venv/bin/activate</span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="plaintext">    $ (paleomix) pip install --upgrade paleomix</span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="plaintext">    $ (paleomix) deactivate</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="80" 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="LC75" class="line" lang="plaintext">    $ ./venv/bin/pip install --upgrade paleomix</span>

</pre>

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<pre style="margin: 0;"> <span id="LC76" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="plaintext">Conda installation</span>

</pre>

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="plaintext">------------------<span class="idiff left right">-</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="79" 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="LC79" class="line" lang="plaintext">------------------</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="84" 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="LC80" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="85" 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="LC81" class="line" lang="plaintext">To have a completely contained environment that includes all software dependencies, you can create a `conda`_ environment.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" 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">@@ -100,19 +96,13 @@ You can now activate the paleomix environment with::</td>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext">    $ conda activate paleomix</span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="plaintext">Next, install PALEOMIX in the activated environment using pip:</span>

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<pre style="margin: 0;">-<span id="LC104" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="plaintext">.. parsed-literal::</span>

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="plaintext">    $ (paleomix) pip install paleomix==\ |release|</span>

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<pre style="margin: 0;">-<span id="LC108" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC99" class="line" lang="plaintext">PALEOMIX requires that the Picard JAR file can be found in a specific location, so we can symlink the versions in your conda environment into the correct place::</span>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="plaintext">    $ (paleomix) mkdir -p ~/install/jar_root/</span>

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<pre style="margin: 0;">-<span id="LC112" class="line" lang="plaintext">    $ (paleomix) ln -s ~/<span class="idiff left right">mini</span>conda*/envs/paleomix/share/picard-*/picard.jar ~/install/jar_root/</span>

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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">    $ (paleomix) ln -s ~/<span class="idiff left right">*</span>conda*/envs/paleomix/share/picard-*/picard.jar ~/install/jar_root/</span>

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="plaintext">.. note::</span>

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="plaintext">    If you installed <span class="idiff left right">mini</span>conda in a different location, then you can obtain the location of the `paleomix` environment by running `conda env list`.</span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="105" 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="LC105" class="line" lang="plaintext">    If you installed conda in a different location, then you can obtain the location of the `paleomix` environment by running `conda env list`.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC106" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="plaintext">Once completed, you can test the environment works correctly using the pipeline test commands described in :ref:`examples`.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="plaintext"></span>

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<li id="ce077518f2a097c8a27352216388e17ae9d5bb9a">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#ce077518f2a097c8a27352216388e17ae9d5bb9a"><strong>docs/other_tools.rst</strong></a>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">Other tools</span>

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">On top of the pipelines described in the major sections of the documentation, the pipeline comes bundled with several other, smaller tools, all accessible via the <span class="idiff left">'</span>paleomix<span class="idiff right">'</span> command. These tools are (briefly) described in this section.</span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">On top of the pipelines described in the major sections of the documentation, the pipeline comes bundled with several other, smaller tools, all accessible via the <span class="idiff left">`</span>paleomix<span class="idiff right">`</span> command. These tools are (briefly) described in this section.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">paleomix coverage</span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="21" 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">@@ -21,15 +21,15 @@ Calculates a depth histogram for a BAM file, either for the entire genome or for</td>

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">paleomix rmdup_collapsed</span>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">------------------------</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">Filters PCR duplicates for merged/collapsed paired-ended reads, such as those generated by AdapterRemoval with the --collapse option enabled. Unlike `SAMtools rmdup` or `Picard MarkDuplicates`, this tool identifies duplicates based on both the 5' and the 3' alignment coordinates of individual reads.</span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">Filters PCR duplicates for merged/collapsed paired-ended reads, such as those generated by AdapterRemoval with the <span class="idiff left">`</span>--collapse<span class="idiff right">`</span> option enabled. Unlike `SAMtools rmdup` or `Picard MarkDuplicates`, this tool identifies duplicates based on both the 5' and the 3' alignment coordinates of individual reads.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">paleomix vcf_filter</span>

</pre>

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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>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext">Quality filters for VCF records, similar to <span class="idiff left">'</span>vcfutils.pl varFilter<span class="idiff right">'</span>.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Quality filters for VCF records, similar to <span class="idiff left">`</span>vcfutils.pl varFilter<span class="idiff right">`</span>.</span>

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">paleomix vcf_to_fasta</span>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">---------------------</span>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">The 'paleomix vcf\_to\_fasta' command is used to generate FASTA sequences from a VCF file, based either on a set of BED coordinates provided by the user, or for the entire genome covered by the VCF file. By default, heterzyous SNPs are represented using IUPAC codes.</span></pre>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">The 'paleomix vcf\_to\_fasta' command is used to generate FASTA sequences from a VCF file, based either on a set of BED coordinates provided by the user, or for the entire genome covered by the VCF file. By default, heter<span class="idiff left">o</span>zy<span class="idiff right">g</span>ous SNPs are represented using IUPAC codes.</span></pre>

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<br>

</li>

<li id="932db922e46b10de6ec4bf49dcb26a3baa73cef8">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#932db922e46b10de6ec4bf49dcb26a3baa73cef8"><strong>docs/yaml.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">@@ -7,17 +7,17 @@ YAML usage in PALEOMIX</td>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">`YAML`_ is a simple markup language adopted for use in configuration files by pipelines included in PALEOMIX. YAML was chosen because it is a plain-text format that is easy to read and write by hand. Since YAML files are plain-text, they may be edited using any standard text editors, with the following caveats:</span>

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">* YAML exclusively uses spaces for indentation, not tabs; attempting to use tabs in YAML files will cause failures when the file is read by the pipelines.</span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">* YAML is case-sensitive; an option such as <span class="idiff left">'</span>QualityOffset<span class="idiff">'</span> is not the same as <span class="idiff">'</span>qualityoffset<span class="idiff right">'</span>.</span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">* It is strongly recommended that all files be named using the <span class="idiff left">'</span>.yaml<span class="idiff right">'</span> file-extension; setting the extension helps ensure proper handling by editors that natively support the YAML format.</span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">* YAML is case-sensitive; an option such as <span class="idiff left">`</span>QualityOffset<span class="idiff">`</span> is not the same as <span class="idiff"> `</span>qualityoffset<span class="idiff right">`</span>.</span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">* It is strongly recommended that all files be named using the <span class="idiff left">`</span>.yaml<span class="idiff right">`</span> file-extension; setting the extension helps ensure proper handling by editors that natively support the YAML format.</span>

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

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Only a subset of YAML features are actually used by PALEOMIX, which are described below. These include **mappings**, by which values are identified by names; **lists** of values; and **numbers**, **text-strings**, and **true** / **false** values, typically representing program options, file-paths, and the like. In addition, comments prefixed by the hash-sign (<span class="idiff left right">#</span>) are frequently used to provide documentation.</span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Only a subset of YAML features are actually used by PALEOMIX, which are described below. These include **mappings**, by which values are identified by names; **lists** of values; and **numbers**, **text-strings**, and **true** / **false** values, typically representing program options, file-paths, and the like. In addition, comments prefixed by the hash-sign (<span class="idiff left right">`#`</span>) are frequently used to provide documentation.</span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></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">Comments</span>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">--------</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">Comments are specified by prefixing unquoted text with the hash-sign (<span class="idiff left right">#</span>); all comments are ignored, and have no effect on the operation of the program. Comments are used solely to document the YAML files used by the pipelines::</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Comments are specified by prefixing unquoted text with the hash-sign (<span class="idiff left right">`#`</span>); all comments are ignored, and have no effect on the operation of the program. Comments are used solely to document the YAML files used by the pipelines::</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">    # This is a comment; the next line contains both a value and a comment:</span>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">    123  # Comments may be placed on the same line as values.</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" 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="63" 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">@@ -63,7 +63,7 @@ And similarly, the following values are all interpreted as *false*::</td>

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">    no</span>

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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">    off</span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="plaintext">Template files included with the pipelines mostly use <span class="idiff left">'</span>yes<span class="idiff">'</span> and <span class="idiff">'</span>no<span class="idiff right">'</span>, but either of the above corresponding values may be used. Note however that none of these values are quoted: If single or double-quotations were used, then these vales would be read as text rather than truth-values, as described next.</span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">Template files included with the pipelines mostly use <span class="idiff left">`</span>yes<span class="idiff">`</span> and <span class="idiff">`</span>no<span class="idiff right">`</span>, but either of the above corresponding values may be used. Note however that none of these values are quoted: If single or double-quotations were used, then these vales would be read as text rather than truth-values, as described next.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="plaintext"></span>

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<td class="old_line diff-line-num" data-linenumber="69" 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="LC69" class="line" lang="plaintext">Text (strings)</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="90" 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="90" 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">@@ -90,7 +90,7 @@ For most part it is not necessary to use quotation marks, and the above could in</td>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="plaintext">    /path/to/my/files/reads.fastq</span>

</pre>

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<pre style="margin: 0;"> <span id="LC92" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="plaintext">However, it is important to make sure that values that are intended to be used strings are not mis<span class="idiff left right">-</span>interpreted as a different type of value. For example, without the quotation marks the following values would be interpreted as numbers or truth-values::</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="94" 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="93" 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="LC93" class="line" lang="plaintext">However, it is important to make sure that values that are intended to be used strings are not misinterpreted as a different type of value. For example, without the quotation marks the following values would be interpreted as numbers or truth-values::</span>

</pre>

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<pre style="margin: 0;"> <span id="LC94" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC95" class="line" lang="plaintext">    "true"</span>

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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="137" 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="137" 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">@@ -137,7 +137,7 @@ Mappings can be nested any number of times, which is used in this manner to crea</td>

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<pre style="margin: 0;"> <span id="LC137" class="line" lang="plaintext">        Option1: /path/to/file.fastq</span>

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<pre style="margin: 0;"> <span id="LC138" class="line" lang="plaintext">        Option2: no</span>

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<pre style="margin: 0;"> <span id="LC139" class="line" lang="plaintext"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="140" 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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<td class="new_line diff-line-num old" data-linenumber="140" 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="LC140" class="line" lang="plaintext">Note that the two mappings belonging to the <span class="idiff left">'</span>Option<span class="idiff right">'</span> mapping are both indented the same number of spaces, which is what allows the program to figure out which values belong to what label. It is therefore important to keep indentation consistent.</span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="141" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="140" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">Note that the two mappings belonging to the <span class="idiff left">`</span>Option<span class="idiff right">`</span> mapping are both indented the same number of spaces, which is what allows the program to figure out which values belong to what label. It is therefore important to keep indentation consistent.</span>

</pre>

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<pre style="margin: 0;"> <span id="LC141" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC142" class="line" lang="plaintext">Lists of values</span>

</pre>

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<pre style="margin: 0;"> <span id="LC143" class="line" lang="plaintext">---------------</span>

</pre>

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<br>

</li>

<li id="31db6545668043f26d9d05b8338b53acf3b3c5e1">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#31db6545668043f26d9d05b8338b53acf3b3c5e1"><strong>paleomix/__init__.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,5 +21,5 @@</td>

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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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<td class="old_line diff-line-num" data-linenumber="22" 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="LC22" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>

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<td class="old_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">

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

</pre>

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24

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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">2</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">

24

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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">3</span></span><span class="p">)</span></span>

</pre>

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<td class="old_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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<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="82233c75268e15a595a90e8494933e20039bfa91">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#82233c75268e15a595a90e8494933e20039bfa91"><strong>paleomix/nodes/picard.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" 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="61" 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">@@ -61,7 +61,7 @@ class ValidateBAMNode(PicardNode):</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python">        <span class="n" style="color: #333;">builder</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">picard_command</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="s" style="color: #d14;">"ValidateSamFile"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="62" 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="LC62" class="line" lang="python">        <span class="n" style="color: #333;">_set_max_open_files</span><span class="p">(</span><span class="n" style="color: #333;">builder</span><span class="p">,</span> <span class="s" style="color: #d14;">"MAX_OPEN_TEMP_FILES"</span><span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="63" 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="63" 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="LC63" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="64" 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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<td class="new_line diff-line-num old" data-linenumber="64" 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="LC64" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="bp" style="color: #999;"><span class="idiff left">True</span></span><span class="idiff"> </span><span class="ow" style="font-weight: 600;"><span class="idiff">or</span></span><span class="idiff right"> </span><span class="n" style="color: #333;">big_genome_mode</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="65" 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="64" 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="LC64" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">big_genome_mode</span><span class="p">:</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="65" 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="65" 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="LC65" class="line" lang="python">            <span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_configure_for_big_genome</span><span class="p">(</span><span class="n" style="color: #333;">config</span><span class="p">,</span> <span class="n" style="color: #333;">builder</span><span class="p">)</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="66" 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="LC66" class="line" lang="python"></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="67" 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="67" 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="LC67" class="line" lang="python">        <span class="n" style="color: #333;">builder</span><span class="p">.</span><span class="n" style="color: #333;">set_option</span><span class="p">(</span><span class="s" style="color: #d14;">"I"</span><span class="p">,</span> <span class="s" style="color: #d14;">"%(IN_BAM)s"</span><span class="p">,</span> <span class="n" style="color: #333;">sep</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"="</span><span class="p">)</span></span>

</pre>

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<br>

</li>

<li id="0bb049ed8bfc26bbe651ba505b441330e59eb32e">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#0bb049ed8bfc26bbe651ba505b441330e59eb32e"><strong>paleomix/pipelines/bam/parts/summary.py</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="125" 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="125" 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">@@ -125,7 +125,12 @@ class SummaryTableNode(Node):</td>

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<td class="old_line diff-line-num" data-linenumber="125" 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">

125

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<td class="new_line diff-line-num" data-linenumber="125" 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="LC125" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">_</span><span class="p">,</span> <span class="n" style="color: #333;">prefix</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">in</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">.</span><span class="n" style="color: #333;">_prefixes</span><span class="p">.</span><span class="n" style="color: #333;">items</span><span class="p">()):</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="126" 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="126" 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="LC126" class="line" lang="python">            <span class="n" style="color: #333;">stats</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genomes</span><span class="p">[</span><span class="n" style="color: #333;">prefix</span><span class="p">[</span><span class="s" style="color: #d14;">"Name"</span><span class="p">]]</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="127" 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="LC127" class="line" lang="python">            <span class="n" style="color: #333;">rows</span><span class="p">.</span><span class="n" style="color: #333;">append</span><span class="p">(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="python">                <span class="p">(</span><span class="n" style="color: #333;">prefix</span><span class="p">[</span><span class="s" style="color: #d14;">"Name"</span><span class="p">],</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="s" style="color: #d14;">"NContigs"</span><span class="p">],</span> <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="s" style="color: #d14;">"Size"</span><span class="p">],</span> <span class="n" style="color: #333;">prefix</span><span class="p">[</span><span class="s" style="color: #d14;">"Path"</span><span class="p">],)</span></span>

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<pre style="margin: 0;">+<span id="LC128" class="line" lang="python">                <span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC129" class="line" lang="python">                    <span class="n" style="color: #333;">prefix</span><span class="p">[</span><span class="s" style="color: #d14;">"Name"</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="python">                    <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="s" style="color: #d14;">"NContigs"</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="python">                    <span class="n" style="color: #333;">stats</span><span class="p">[</span><span class="s" style="color: #d14;">"Size"</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC132" class="line" lang="python">                    <span class="n" style="color: #333;">prefix</span><span class="p">[</span><span class="s" style="color: #d14;">"Path"</span><span class="p">],</span></span>

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<pre style="margin: 0;">+<span id="LC133" class="line" lang="python">                <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC134" class="line" lang="python">            <span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC135" class="line" lang="python"></span>

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<pre style="margin: 0;"> <span id="LC136" class="line" lang="python">        <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">line</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">text</span><span class="p">.</span><span class="n" style="color: #333;">padded_table</span><span class="p">(</span><span class="n" style="color: #333;">rows</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">@@ -248,19 +253,19 @@ class SummaryTableNode(Node):</td>

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<pre style="margin: 0;"> <span id="LC253" class="line" lang="python">                <span class="n" style="color: #333;">total_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">subtables</span><span class="p">.</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"reads"</span><span class="p">,</span> <span class="p">{}).</span><span class="n" style="color: #333;">get</span><span class="p">(</span><span class="s" style="color: #d14;">"seq_retained_reads"</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">)</span></span>

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<pre style="margin: 0;"> <span id="LC254" class="line" lang="python">                <span class="n" style="color: #333;">genome_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">genomes</span><span class="p">[</span><span class="n" style="color: #333;">tblname</span><span class="p">][</span><span class="s" style="color: #d14;">"Size"</span><span class="p">]</span></span>

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<pre style="margin: 0;"> <span id="LC255" class="line" lang="python"></span>

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<pre style="margin: 0;">-<span id="LC251" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_raw_frac(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_hits</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span></span>

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<pre style="margin: 0;">+<span id="LC256" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_raw_frac(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_hits</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">float</span></span><span class="p">(</span></span>

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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python">                    <span class="n" style="color: #333;">total_reads</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"NaN"</span></span>

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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python">                <span class="p">)</span></span>

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<pre style="margin: 0;">-<span id="LC254" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_unique_frac(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_uniq</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num new" data-linenumber="259" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_unique_frac(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_uniq</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">float</span></span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="255" 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="LC260" class="line" lang="python">                    <span class="n" style="color: #333;">total_reads</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"NaN"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python">                <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="257" 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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<td class="new_line diff-line-num old" data-linenumber="262" 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="LC257" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_clonality(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">total_uniq</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="258" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="262" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC262" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_clonality(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">total_uniq</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">float</span></span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="263" 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="LC263" class="line" lang="python">                    <span class="n" style="color: #333;">total_hits</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"NaN"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC264" class="line" lang="python">                <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="260" 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="LC260" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_length(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_nts</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="265" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC265" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_length(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_nts</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">float</span></span><span class="p">(</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="266" 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="LC266" class="line" lang="python">                    <span class="n" style="color: #333;">total_uniq</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"NaN"</span></span>

</pre>

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<td class="new_line diff-line-num" data-linenumber="267" 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="LC267" class="line" lang="python">                <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="263" 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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<td class="new_line diff-line-num old" data-linenumber="268" 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="LC263" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_coverage(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_nts</span> <span class="o" style="font-weight: 600;">/</span> <span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num new" data-linenumber="264" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<td class="new_line diff-line-num new" data-linenumber="268" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC268" class="line" lang="python">                <span class="n" style="color: #333;">subtable</span><span class="p">[</span><span class="s" style="color: #d14;">"hits_coverage(%s)"</span> <span class="o" style="font-weight: 600;">%</span> <span class="n" style="color: #333;">tblname</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">total_nts</span> <span class="o" style="font-weight: 600;">/</span> <span class="nb" style="color: #0086b3;"><span class="idiff left right">float</span></span><span class="p">(</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="264" 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="269" 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="LC269" class="line" lang="python">                    <span class="n" style="color: #333;">genome_size</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">"NaN"</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="265" 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="270" 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="LC270" class="line" lang="python">                <span class="p">)</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="266" 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="271" 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="LC271" class="line" lang="python"></span>

</pre>

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<br>

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<li id="05b9434c6f6c420942ce278e6fed40fa39b01fe1">

<a href="https://salsa.debian.org/med-team/paleomix/-/commit/f9367bda9d3b082439d3137ae2dfd2a7f12802e6#05b9434c6f6c420942ce278e6fed40fa39b01fe1"><strong>paleomix_environment.yaml</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ dependencies:</td>

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<td class="old_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

7

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">adapterremoval>=2.2.0</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<td class="new_line diff-line-num" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

8

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">samtools>=1.3.0</span></span>

</pre>

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<td class="old_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">

9

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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">

9

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">picard>=1.137</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="10" 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">

10

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<td class="new_line diff-line-num old" data-linenumber="10" 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="LC10" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">bowtie2>=2.3.0</span></span>

</pre>

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<td class="old_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">

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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">

10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">bowtie2>=2.3.0<span class="idiff left right">,<2.4.0</span></span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="11" 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">

11

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<td class="new_line diff-line-num" data-linenumber="11" 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">

11

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">bwa>=0.7.15</span></span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<td class="new_line diff-line-num" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

12

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">mapdamage2>=2.2.1</span></span>

</pre>

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<td class="old_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">

13

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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">

13

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">r-base</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" 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="16" 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">@@ -16,4 +16,4 @@ dependencies:</td>

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<td class="old_line diff-line-num" data-linenumber="16" 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">

16

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<td class="new_line diff-line-num" data-linenumber="16" 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">

16

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="yaml">  <span class="pi">-</span> <span class="s" style="color: #d14;">r-gam</span></span>

</pre>

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<td class="old_line diff-line-num" 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">

17

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<td class="new_line diff-line-num" 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">

17

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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-inline</span></span>

</pre>

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<td class="old_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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<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="na" style="color: #008080;">pip</span><span class="pi">:</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="19" 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">

19

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<td class="new_line diff-line-num old" data-linenumber="19" 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="LC19" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">paleomix==1.3.<span class="idiff left right">2</span></span></span></pre>

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<td class="old_line diff-line-num new" data-linenumber="20" 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="19" 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">

19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">paleomix==1.3.<span class="idiff left right">3</span></span></span></pre>

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