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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/ataqv">Debian Med / ataqv</a>
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<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df">7e5d5230</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-10-01T13:24:21+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.2.1+ds</pre>
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<h4>12 changed files:</h4>
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<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#561b88e19de321ca62c7590bbb350765fb110905">
README.rst
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<li class="file-stats">
<a href="#874220bbb90ee2bce3a1a7012aa59a4a7ca5cefe">
src/cpp/HTS.cpp
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<li class="file-stats">
<a href="#35cfc5765350823237a91d569a36103a527e8902">
src/cpp/Metrics.cpp
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<li class="file-stats">
<a href="#c64a1451699a98bd94546aaeec7f24766ca577cc">
src/cpp/Metrics.hpp
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<li class="file-stats">
<a href="#829c892bd31c9fd71c2b6bdaeea37d33bd08ff2b">
src/cpp/Version.hpp
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<li class="file-stats">
<a href="#f3a91c0ac2e82bba3bafd4d781627f999fb4a1ed">
src/cpp/ataqv.cpp
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<li class="file-stats">
<a href="#1c19518fdf829f768d296d9dfef789b5c61cc9a5">
src/cpp/test_metrics.cpp
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<li class="file-stats">
<a href="#30626a8b87bc9f6d91bf1d3fb6b81ff29b39b1a8">
src/scripts/mkarv
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<li class="file-stats">
<a href="#e457e356e5bbbb4b33c5ac0a6a123f3c5d1476f4">
src/web/index.html
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<li class="file-stats">
<a href="#3d6e52c1c03d213496ef289d51d3aa940e4de480">
src/web/js/ataqv.js
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<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,6 +2,8 @@</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">build</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">testing</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">README.html</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">debian/.debhelper</span>
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<td class="diff-line-num new new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">debian/ataqv.debhelper.log</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">debian/ataqv.substvars</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">debian/ataqv/</span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">debian/debhelper-build-stamp</span>
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<li id="836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,7 +2,7 @@</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># VARIABLES</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 1.<span class="idiff left right">1</span>.1</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="make"><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> 1.<span class="idiff left right">2</span>.1</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<td class="diff-line-num new_line" 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">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># PATHS</span></span>
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<li id="561b88e19de321ca62c7590bbb350765fb110905">
<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#561b88e19de321ca62c7590bbb350765fb110905"><strong>README.rst</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,6 +54,12 @@ Help</td>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="plaintext">If you have questions or suggestions, mail us at</span>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="plaintext">`parkerlab-software@umich.edu`_, or file a `GitHub issue`_.</span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext"></span>
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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">Citing</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"></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">Ataqv is now published in Cell Systems: https://doi.org/10.1016/j.cels.2020.02.009</span>
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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">***************</span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="plaintext">Getting started</span>
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<pre style="margin: 0;"> <span id="LC65" 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">@@ -203,8 +209,59 @@ for the output.</td>
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<pre style="margin: 0;"> <span id="LC209" class="line" lang="plaintext">Running</span>
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<pre style="margin: 0;"> <span id="LC210" class="line" lang="plaintext">=======</span>
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<pre style="margin: 0;"> <span id="LC211" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="plaintext">The main program is ataqv. Run ``ataqv --help`` for complete</span>
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<pre style="margin: 0;">-<span id="LC207" class="line" lang="plaintext">instructions.</span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">The main program is ataqv, which is run as follows::</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext"> ataqv [options] organism alignment-file</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext"> where:</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext"> organism is the subject of the experiment, which determines the list of autosomes</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext"> (see "Reference Genome Configuration" below).</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext"> alignment-file is a BAM file with duplicate reads marked.</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext"> Basic options</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="LC224" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext"> --help: show this usage message.</span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext"> --verbose: show more details and progress updates.</span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext"> --version: print the version of the program.</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext"> --threads <n>: the maximum number of threads to use (right now, only for calculating TSS enrichment).</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext"> Optional Input</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext"> --------------</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext"> --peak-file "file name"</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext"> A BED file of peaks called for alignments in the BAM file. Specify "auto" to use the</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext"> BAM file name with ".peaks" appended, or if the BAM file contains read groups, to</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext"> assume each read group has a peak file whose name is the read group ID with ".peaks"</span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext"> appended. If you specify a single filename instead of "auto" with read groups, the </span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext"> same peaks will be used for all reads -- be sure this is what you want.</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"> --tss-file "file name"</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext"> A BED file of transcription start sites for the experiment organism. If supplied,</span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext"> a TSS enrichment score will be calculated according to the ENCODE data standards.</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext"> This calculation requires that the BAM file of alignments be indexed.</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext"> --tss-extension "size"</span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext"> If a TSS enrichment score is requested, it will be calculated for a region of </span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext"> "size" bases to either side of transcription start sites. The default is 1000bp.</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext"> </span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext"> --excluded-region-file "file name"</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext"> A BED file containing excluded regions. Peaks or TSS overlapping these will be ignored.</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext"> May be given multiple times.</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="LC253" class="line" lang="plaintext"> Output</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"> </span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext"> --metrics-file "file name"</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext"> The JSON file to which metrics will be written. The default filename will be based on</span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext"> the BAM file, with the suffix ".ataqv.json".</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext"> --log-problematic-reads</span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext"> If given, problematic reads will be logged to a file per read group, with names</span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext"> derived from the read group IDs, with ".problems" appended. If no read groups</span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext"> are found, the reads will be written to one file named after the BAM file.</span>
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext"></span>
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208
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<pre style="margin: 0;"> <span id="LC265" class="line" lang="plaintext"></span>
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209
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<pre style="margin: 0;"> <span id="LC266" class="line" lang="plaintext">When run, ataqv prints a human-readable summary to its standard</span>
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210
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<pre style="margin: 0;"> <span id="LC267" class="line" lang="plaintext">output, and writes complete metrics to the JSON file named with the</span>
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<li id="874220bbb90ee2bce3a1a7012aa59a4a7ca5cefe">
<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#874220bbb90ee2bce3a1a7012aa59a4a7ca5cefe"><strong>src/cpp/HTS.cpp</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">@@ -37,7 +37,7 @@ sam_header parse_sam_header(const std::string &header_text) {</td>
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37
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37
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">stringstream</span> <span class="n" style="color: #333;">field_stream</span><span class="p">(</span><span class="n" style="color: #333;">field</span><span class="p">);</span></span>
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38
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">field_text</span><span class="p">;</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">getline</span><span class="p">(</span><span class="n" style="color: #333;">field_stream</span><span class="p">,</span> <span class="n" style="color: #333;">field_text</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);)</span> <span class="p">{</span></span>
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39
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">splitfield</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">split</span><span class="p">(</span><span class="n" style="color: #333;">field_text</span><span class="p">,</span> <span class="s" style="color: #d14;">":"</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">field_map</span><span class="p">[</span><span class="n" style="color: #333;">splitfield</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">splitfield</span><span class="p"><span class="idiff left">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff right">]</span>;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">field_map</span><span class="p">[</span><span class="n" style="color: #333;">splitfield</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">splitfield</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">size</span></span><span class="p"><span class="idiff">()</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">></span></span><span class="idiff"> </span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">?</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">splitfield</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">:</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff right">""</span></span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">header</span><span class="p">[</span><span class="n" style="color: #333;">header_tag</span><span class="p">].</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">field_map</span><span class="p">);</span></span>
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<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#35cfc5765350823237a91d569a36103a527e8902"><strong>src/cpp/Metrics.cpp</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">@@ -37,6 +37,7 @@ MetricsCollector::MetricsCollector(const std::string& name,</td>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_limit</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ignore_read_groups</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">log_problematic_reads</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">less_redundant</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC41" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">excluded_region_filenames</span><span class="p">)</span> <span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"> <span class="n" style="color: #333;">metrics</span><span class="p">({}),</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">name</span><span class="p">(</span><span class="n" style="color: #333;">name</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">@@ -54,6 +55,7 @@ MetricsCollector::MetricsCollector(const std::string& name,</td>
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<pre style="margin: 0;"> <span id="LC55" class="line" lang="cpp"> <span class="n" style="color: #333;">thread_limit</span><span class="p">(</span><span class="n" style="color: #333;">thread_limit</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="cpp"> <span class="n" style="color: #333;">ignore_read_groups</span><span class="p">(</span><span class="n" style="color: #333;">ignore_read_groups</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"> <span class="n" style="color: #333;">log_problematic_reads</span><span class="p">(</span><span class="n" style="color: #333;">log_problematic_reads</span><span class="p">),</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="cpp"> <span class="n" style="color: #333;">less_redundant</span><span class="p">(</span><span class="n" style="color: #333;">less_redundant</span><span class="p">),</span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="cpp"> <span class="n" style="color: #333;">excluded_region_filenames</span><span class="p">(</span><span class="n" style="color: #333;">excluded_region_filenames</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"></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">@@ -425,7 +427,7 @@ void MetricsCollector::load_alignments() {</td>
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<pre style="margin: 0;"> <span id="LC427" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC429" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC428" class="line" lang="cpp"><span class="n" style="color: #333;">Metrics</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Metrics</span><span class="p">(</span><span class="n" style="color: #333;">MetricsCollector</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">collector</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">name</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">collector</span><span class="p">),</span> <span class="n" style="color: #333;">name</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="n" style="color: #333;">peaks</span><span class="p">(),</span> <span class="n" style="color: #333;">log_problematic_reads</span><span class="p">(</span><span class="n" style="color: #333;">collector</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">log_problematic_reads</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="cpp"><span class="n" style="color: #333;">Metrics</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">Metrics</span><span class="p">(</span><span class="n" style="color: #333;">MetricsCollector</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">collector</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">name</span><span class="p">)</span><span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">collector</span><span class="p">),</span> <span class="n" style="color: #333;">name</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">),</span> <span class="n" style="color: #333;">peaks</span><span class="p">(),</span> <span class="n" style="color: #333;">log_problematic_reads</span><span class="p">(</span><span class="n" style="color: #333;">collector</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">log_problematic_reads</span><span class="p">)<span class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">less_redundant</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">collector</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="n" style="color: #333;"><span class="idiff">less_redundant</span></span><span class="p"><span class="idiff right">)</span></span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC431" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC432" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">log_problematic_reads</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC433" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">try</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">@@ -1252,11 +1254,13 @@ std::ostream& operator<<(std::ostream& os, const Metrics& m) {</td>
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<pre style="margin: 0;"> <span id="LC1254" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC1255" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1256" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Aberrant Mapping Metrics"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1255" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ------------------------"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1256" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" RF reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rf_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rf_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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1257
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<pre style="margin: 0;">-<span id="LC1257" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" FF reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">ff_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">ff_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1258" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" RR reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rr_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rr_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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1259
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<pre style="margin: 0;">-<span id="LC1259" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Reads that paired and mapped but..."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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1257
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<pre style="margin: 0;">+<span id="LC1257" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ------------------------"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1258
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<pre style="margin: 0;">+<span id="LC1258" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">less_redundant</span><span class="p">)</span> <span class="p">{</span></span>
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1259
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<pre style="margin: 0;">+<span id="LC1259" class="line" lang="cpp"> <span class="n" style="color: #333;">os</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" RF reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rf_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rf_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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1260
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<pre style="margin: 0;">+<span id="LC1260" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" FF reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">ff_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">ff_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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1261
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<pre style="margin: 0;">+<span id="LC1261" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" RR reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rr_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">rr_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">6</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1262
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<pre style="margin: 0;">+<span id="LC1262" class="line" lang="cpp"> <span class="p">}</span></span>
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1263
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<pre style="margin: 0;">+<span id="LC1263" class="line" lang="cpp"> <span class="n" style="color: #333;">os</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Reads that paired and mapped but..."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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1260
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1264
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<pre style="margin: 0;"> <span id="LC1264" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" on different chromosomes: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">reads_with_mate_mapped_to_different_reference</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">reads_with_mate_mapped_to_different_reference</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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1261
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1265
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<pre style="margin: 0;"> <span id="LC1265" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" probably too far from their mates: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">reads_with_mate_too_distant</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">reads_with_mate_too_distant</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" (longest proper fragment seems to be "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">maximum_proper_pair_fragment_size</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">")"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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1262
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1266
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<pre style="margin: 0;"> <span id="LC1266" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setfill</span><span class="p">(</span><span class="sc" style="color: #d14;">' '</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">left</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">setw</span><span class="p">(</span><span class="mi" style="color: #099;">40</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" just not properly: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">reads_mapped_and_paired_but_improperly</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">reads_mapped_and_paired_but_improperly</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</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">@@ -1264,19 +1268,25 @@ std::ostream& operator<<(std::ostream& os, const Metrics& m) {</td>
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<pre style="margin: 0;"> <span id="LC1268" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC1269" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1270" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Autosomal/Mitochondrial Metrics"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1267" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -------------------------------"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1268" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Total autosomal reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_autosomal_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_autosomal_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">" ("</span><span class="p">,</span> <span class="s" style="color: #d14;">"% of all reads)"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1269" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Total mitochondrial reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_mitochondrial_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_mitochondrial_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">" ("</span><span class="p">,</span> <span class="s" style="color: #d14;">"% of all reads)"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1270" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Duplicate autosomal reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">duplicate_autosomal_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">duplicate_autosomal_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_autosomal_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">" ("</span><span class="p">,</span> <span class="s" style="color: #d14;">"% of all autosomal reads)"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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1271
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<pre style="margin: 0;">-<span id="LC1271" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Duplicate mitochondrial reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">duplicate_mitochondrial_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">duplicate_mitochondrial_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_mitochondrial_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">" ("</span><span class="p">,</span> <span class="s" style="color: #d14;">"% of all mitochondrial reads)"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC1271" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" -------------------------------"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">less_redundant</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1273" class="line" lang="cpp"> <span class="n" style="color: #333;">os</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Total autosomal reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_autosomal_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_autosomal_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">" ("</span><span class="p">,</span> <span class="s" style="color: #d14;">"% of all reads)"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1274" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1275" class="line" lang="cpp"> <span class="n" style="color: #333;">os</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Total mitochondrial reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_mitochondrial_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_mitochondrial_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">" ("</span><span class="p">,</span> <span class="s" style="color: #d14;">"% of all reads)"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC1276" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Duplicate autosomal reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">duplicate_autosomal_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">duplicate_autosomal_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_autosomal_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">" ("</span><span class="p">,</span> <span class="s" style="color: #d14;">"% of all autosomal reads)"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">less_redundant</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1278" class="line" lang="cpp"> <span class="n" style="color: #333;">os</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Duplicate mitochondrial reads: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">duplicate_mitochondrial_reads</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">percentage_string</span><span class="p">(</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">duplicate_mitochondrial_reads</span><span class="p">,</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">total_mitochondrial_reads</span><span class="p">,</span> <span class="mi" style="color: #099;">3</span><span class="p">,</span> <span class="s" style="color: #d14;">" ("</span><span class="p">,</span> <span class="s" style="color: #d14;">"% of all mitochondrial reads)"</span><span class="p">)</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1279" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC1280" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC1273" class="line" lang="cpp"> <span class="idiff left right"> </span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC1281" class="line" lang="cpp"> <span class="n" style="color: #333;"><span class="idiff left right">os</span></span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC1282" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC1283" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Mapping Quality"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1276" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ---------------"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1277" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Mean MAPQ: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fixed</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">mean_mapq</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1278" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Median MAPQ: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fixed</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">median_mapq</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">-<span id="LC1279" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Reads with MAPQ >=..."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1284" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" ---------------"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">less_redundant</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC1286" class="line" lang="cpp"> <span class="n" style="color: #333;">os</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Mean MAPQ: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fixed</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">mean_mapq</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC1287" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Median MAPQ: "</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">fixed</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">m</span><span class="p">.</span><span class="n" style="color: #333;">median_mapq</span><span class="p">()</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC1288" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC1289" class="line" lang="cpp"> <span class="n" style="color: #333;">os</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" Reads with MAPQ >=..."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span><span class="p">;</span></span>
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1280
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1290
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<pre style="margin: 0;"> <span id="LC1290" class="line" lang="cpp"></span>
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1281
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1291
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<pre style="margin: 0;"> <span id="LC1291" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">5</span><span class="p">;</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;"><=</span> <span class="mi" style="color: #099;">30</span><span class="p">;</span> <span class="n" style="color: #333;">threshold</span> <span class="o" style="font-weight: 600;">+=</span> <span class="mi" style="color: #099;">5</span><span class="p">)</span> <span class="p">{</span></span>
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1282
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1292
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<pre style="margin: 0;"> <span id="LC1292" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">long</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">count</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#c64a1451699a98bd94546aaeec7f24766ca577cc"><strong>src/cpp/Metrics.hpp</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">@@ -66,6 +66,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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67
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67
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ignore_read_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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68
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68
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">log_problematic_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">less_redundant</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">excluded_region_filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{};</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">Feature</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">excluded_regions</span> <span class="o" style="font-weight: 600;">=</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">@@ -85,6 +86,7 @@ public:</td>
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86
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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span></span>
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86
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87
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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ignore_read_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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88
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">log_problematic_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">less_redundant</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span></span>
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88
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">vector</span><span class="o" style="font-weight: 600;"><</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">excluded_region_filenames</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{});</span></span>
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91
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="cpp"></span>
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92
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">autosomal_reference_string</span><span class="p">(</span><span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">separator</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">", "</span><span class="p">)</span> <span class="k" style="font-weight: 600;">const</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">@@ -198,6 +200,7 @@ public:</td>
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<pre style="margin: 0;"> <span id="LC200" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">log_problematic_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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199
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201
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<pre style="margin: 0;"> <span id="LC201" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">peaks_requested</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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202
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<pre style="margin: 0;"> <span id="LC202" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">tss_requested</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">less_redundant</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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204
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"> <span class="n" style="color: #333;">Metrics</span><span class="p">(</span><span class="n" style="color: #333;">MetricsCollector</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">collector</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC206" class="line" lang="cpp"></span>
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<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#829c892bd31c9fd71c2b6bdaeea37d33bd08ff2b"><strong>src/cpp/Version.hpp</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">@@ -4,4 +4,4 @@</td>
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// Licensed under Version 3 of the GPL or any later version</span></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "1.<span class="idiff left right">1</span>.1"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define VERSION "1.<span class="idiff left right">2</span>.1"</span></span></pre>
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<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#f3a91c0ac2e82bba3bafd4d781627f999fb4a1ed"><strong>src/cpp/ataqv.cpp</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">@@ -38,6 +38,7 @@ enum {</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_METRICS_FILE</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_LOG_PROBLEMATIC_READS</span><span class="p">,</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_LESS_REDUNDANT</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_NAME</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="cpp"> <span class="n" style="color: #333;">OPT_IGNORE_READ_GROUPS</span><span class="p">,</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="111" 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="112" 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">@@ -111,7 +112,10 @@ void print_usage() {</td>
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112
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"--log-problematic-reads"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" If given, problematic reads will be logged to a file per read group, with names"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" derived from the read group IDs, with </span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;">.problems</span><span class="se" style="color: #d14;">\"</span><span class="s" style="color: #d14;"> appended. If no read groups"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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114
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<pre style="margin: 0;">-<span id="LC114" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" are found, the reads will be written to one file named after the BAM file."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" are found, the reads will be written to one file named after the BAM file."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="cpp"></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"--less-redundant"</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">" If given, output a subset of metrics that should be less redundant. If this flag is used, the same flag should be passed to mkarv when making the viewer."</span> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="o" style="font-weight: 600;"><<</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">endl</span></span>
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="212" 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">@@ -212,6 +216,7 @@ int main(int argc, char **argv) {</td>
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<pre style="margin: 0;"> <span id="LC216" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">verbose</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC217" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">thread_limit</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC218" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">log_problematic_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">less_redundant</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">name</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">bool</span> <span class="n" style="color: #333;">ignore_read_groups</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="238" 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">@@ -238,6 +243,7 @@ int main(int argc, char **argv) {</td>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"version"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_VERSION</span><span class="p">},</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"threads"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_THREADS</span><span class="p">},</span></span>
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240
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245
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"log-problematic-reads"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_LOG_PROBLEMATIC_READS</span><span class="p">},</span></span>
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<td class="diff-line-num new old_line" data-linenumber="241" 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="diff-line-num new new_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"less-redundant"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_LESS_REDUNDANT</span><span class="p">},</span></span>
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241
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<td class="diff-line-num new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;"> <span id="LC247" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"name"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_NAME</span><span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="242" 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">
242
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<td class="diff-line-num new_line" data-linenumber="248" 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">
248
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"ignore-read-groups"</span><span class="p">,</span> <span class="n" style="color: #333;">no_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_IGNORE_READ_GROUPS</span><span class="p">},</span></span>
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<td class="diff-line-num old_line" data-linenumber="243" 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">
243
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<td class="diff-line-num new_line" data-linenumber="249" 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">
249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"> <span class="p">{</span><span class="s" style="color: #d14;">"description"</span><span class="p">,</span> <span class="n" style="color: #333;">required_argument</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">nullptr</span><span class="p">,</span> <span class="n" style="color: #333;">OPT_DESCRIPTION</span><span class="p">},</span></span>
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<td class="diff-line-num unfold js-unfold old_line" 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="277" 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">@@ -271,6 +277,9 @@ int main(int argc, char **argv) {</td>
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<td class="diff-line-num old_line" 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">
271
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<td class="diff-line-num new_line" data-linenumber="277" 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">
277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_LOG_PROBLEMATIC_READS</span><span class="p">:</span></span>
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<td class="diff-line-num old_line" data-linenumber="272" 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">
272
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<td class="diff-line-num new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="n" style="color: #333;">log_problematic_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num old_line" data-linenumber="273" 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">
273
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<td class="diff-line-num new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;"> <span id="LC279" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_LESS_REDUNDANT</span><span class="p">:</span></span>
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<td class="diff-line-num new new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp"> <span class="n" style="color: #333;">less_redundant</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="282" 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">
282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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274
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283
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<pre style="margin: 0;"> <span id="LC283" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">case</span> <span class="n" style="color: #333;">OPT_NAME</span><span class="p">:</span></span>
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275
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<td class="diff-line-num new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;"> <span id="LC284" class="line" lang="cpp"> <span class="n" style="color: #333;">name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">optarg</span><span class="p">;</span></span>
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276
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285
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<pre style="margin: 0;"> <span id="LC285" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">break</span><span class="p">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="355" 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="364" 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">@@ -355,6 +364,7 @@ int main(int argc, char **argv) {</td>
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355
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364
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<pre style="margin: 0;"> <span id="LC364" class="line" lang="cpp"> <span class="n" style="color: #333;">thread_limit</span><span class="p">,</span></span>
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356
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<td class="diff-line-num new_line" data-linenumber="365" 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">
365
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="cpp"> <span class="n" style="color: #333;">ignore_read_groups</span><span class="p">,</span></span>
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357
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<td class="diff-line-num new_line" data-linenumber="366" 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">
366
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="cpp"> <span class="n" style="color: #333;">log_problematic_reads</span><span class="p">,</span></span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="cpp"> <span class="n" style="color: #333;">less_redundant</span><span class="p">,</span></span>
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358
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368
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="cpp"> <span class="n" style="color: #333;">excluded_region_filenames</span><span class="p">);</span></span>
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359
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369
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="cpp"></span>
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360
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370
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// if the filename for the metrics output wasn't specified,</span></span>
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<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#1c19518fdf829f768d296d9dfef789b5c61cc9a5"><strong>src/cpp/test_metrics.cpp</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">@@ -63,7 +63,7 @@ TEST_CASE("MetricsCollector::test_supplied_references", "[metrics/test_supplied_</td>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="cpp"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">out</span> <span class="o" style="font-weight: 600;"><<</span> <span class="s" style="color: #d14;">"I</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">II</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">III</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="s" style="color: #d14;">"Test collector"</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="s" style="color: #d14;">"test.bam"</span><span class="p">,</span> <span class="n" style="color: #333;">autosomal_reference_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"M"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="s" style="color: #d14;">"Test collector"</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="s" style="color: #d14;">"test.bam"</span><span class="p">,</span> <span class="n" style="color: #333;">autosomal_reference_file</span><span class="p">,</span> <span class="s" style="color: #d14;">"M"</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">remove</span><span class="p">(</span><span class="n" style="color: #333;">autosomal_reference_file</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"></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">@@ -92,7 +92,7 @@ TEST_CASE("Metrics::load_alignments with no excluded regions", "[metrics/load_al</td>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"SRR891275.bam"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"SRR891275.peaks.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff right">false</span></span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="cpp"> <span class="n" style="color: #333;">collector</span><span class="p">.</span><span class="n" style="color: #333;">load_alignments</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="cpp"></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">@@ -108,7 +108,7 @@ TEST_CASE("Metrics::load_alignments", "[metrics/load_alignments]") {</td>
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108
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108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"test.peaks.gz"</span><span class="p">);</span></span>
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109
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109
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<pre style="margin: 0;"> <span id="LC109" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tss_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"hg19.tss.refseq.bed.gz"</span><span class="p">);</span></span>
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110
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<pre style="margin: 0;"> <span id="LC110" class="line" lang="cpp"></span>
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111
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<td class="diff-line-num new_line old" data-linenumber="111" 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="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">tss_file_name</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"exclude.dac.bed.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exclude.duke.bed.gz"</span><span class="p">});</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">tss_file_name</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">false</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="p">{</span><span class="s" style="color: #d14;">"exclude.dac.bed.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exclude.duke.bed.gz"</span><span class="p">});</span></span>
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<pre style="margin: 0;"> <span id="LC112" class="line" lang="cpp"></span>
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113
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="cpp"> <span class="n" style="color: #333;">collector</span><span class="p">.</span><span class="n" style="color: #333;">load_alignments</span><span class="p">();</span></span>
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114
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="183" 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">@@ -183,7 +183,7 @@ TEST_CASE("Metrics::ignore_read_groups", "[metrics/ignore_read_groups]") {</td>
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183
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"test.bam"</span><span class="p">);</span></span>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"test.peaks.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="cpp"></span>
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186
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<td class="diff-line-num new_line old" data-linenumber="186" 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="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"exclude.dac.bed.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exclude.duke.bed.gz"</span><span class="p">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">false</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="p">{</span><span class="s" style="color: #d14;">"exclude.dac.bed.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exclude.duke.bed.gz"</span><span class="p">});</span></span>
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187
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="cpp"></span>
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188
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="cpp"> <span class="n" style="color: #333;">collector</span><span class="p">.</span><span class="n" style="color: #333;">load_alignments</span><span class="p">();</span></span>
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<td class="diff-line-num old_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp"></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">@@ -244,7 +244,7 @@ TEST_CASE("Metrics::missing_peak_file", "[metrics/missing_peak_file]") {</td>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"test.bam"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"notthere.peaks.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC246" class="line" lang="cpp"></span>
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<td class="diff-line-num new_line old" data-linenumber="247" 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="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"exclude.dac.bed.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exclude.duke.bed.gz"</span><span class="p">});</span></span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">false</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="p">{</span><span class="s" style="color: #d14;">"exclude.dac.bed.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exclude.duke.bed.gz"</span><span class="p">});</span></span>
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<pre style="margin: 0;"> <span id="LC248" class="line" lang="cpp"> <span class="n" style="color: #333;">REQUIRE_THROWS_AS</span><span class="p">(</span><span class="n" style="color: #333;">collector</span><span class="p">.</span><span class="n" style="color: #333;">load_alignments</span><span class="p">(),</span> <span class="n" style="color: #333;">FileException</span><span class="p">);</span></span>
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249
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<pre style="margin: 0;"> <span id="LC249" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC250" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="254" 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="254" 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">@@ -254,6 +254,6 @@ TEST_CASE("Metrics::missing_tss_file", "[metrics/missing_ss_file]") {</td>
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254
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<pre style="margin: 0;"> <span id="LC254" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"test.peaks.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC255" class="line" lang="cpp"> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">tss_file_name</span><span class="p">(</span><span class="s" style="color: #d14;">"notthere.bed.gz"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="cpp"></span>
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<td class="diff-line-num old old_line" 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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<pre style="margin: 0;">-<span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">tss_file_name</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="p">{</span><span class="s" style="color: #d14;">"exclude.dac.bed.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exclude.duke.bed.gz"</span><span class="p">});</span></span>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="cpp"> <span class="n" style="color: #333;">MetricsCollector</span> <span class="n" style="color: #333;">collector</span><span class="p">(</span><span class="n" style="color: #333;">name</span><span class="p">,</span> <span class="s" style="color: #d14;">"human"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a collector for unit tests"</span><span class="p">,</span> <span class="s" style="color: #d14;">"a library of brutal tests?"</span><span class="p">,</span> <span class="s" style="color: #d14;">"https://theparkerlab.org"</span><span class="p">,</span> <span class="n" style="color: #333;">alignment_file_name</span><span class="p">,</span> <span class="s" style="color: #d14;">""</span><span class="p">,</span> <span class="s" style="color: #d14;">"chrM"</span><span class="p">,</span> <span class="n" style="color: #333;">peak_file_name</span><span class="p">,</span> <span class="n" style="color: #333;">tss_file_name</span><span class="p">,</span> <span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">true</span><span class="p">,</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">false</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff right"> </span><span class="p">{</span><span class="s" style="color: #d14;">"exclude.dac.bed.gz"</span><span class="p">,</span> <span class="s" style="color: #d14;">"exclude.duke.bed.gz"</span><span class="p">});</span></span>
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258
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258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="cpp"> <span class="n" style="color: #333;">REQUIRE_THROWS_AS</span><span class="p">(</span><span class="n" style="color: #333;">collector</span><span class="p">.</span><span class="n" style="color: #333;">load_alignments</span><span class="p">(),</span> <span class="n" style="color: #333;">FileException</span><span class="p">);</span></span>
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259
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259
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<pre style="margin: 0;"> <span id="LC259" class="line" lang="cpp"><span class="p">}</span></span></pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="256" 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="256" 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">@@ -256,6 +256,7 @@ def parse_arguments():</td>
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256
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256
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<pre style="margin: 0;"> <span id="LC256" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-d'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--description'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'A description for the viewer instance.'</span><span class="p">)</span></span>
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<td class="diff-line-num old_line" data-linenumber="257" 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">
257
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257
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<pre style="margin: 0;"> <span id="LC257" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-f'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--force'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Overwrite the output directory if it exists.'</span><span class="p">)</span></span>
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258
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<td class="diff-line-num new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;"> <span id="LC258" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-i'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--indent'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'If indent is given, JSON output will be pretty-printed and indented.'</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-l'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--less-redundant'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Produce a viewer with fewer metrics (metrics that are expected to be largely redundant will not be displayed.'</span><span class="p">)</span></span>
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259
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<td class="diff-line-num new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;"> <span id="LC260" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-m'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--maximum-fragment-length'</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">type</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">int</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="mi" style="color: #099;">1000</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'The maximum fragment length for which the distance to the reference fragment length count distribution will be measured.'</span><span class="p">)</span></span>
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260
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<td class="diff-line-num new_line" data-linenumber="261" 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">
261
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<pre style="margin: 0;"> <span id="LC261" class="line" lang="python"></span>
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<td class="diff-line-num old_line" data-linenumber="261" 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">
261
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<td class="diff-line-num new_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;"> <span id="LC262" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-p'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--peak-reference'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">"SRR891268"</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="285" 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="286" 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">@@ -285,7 +286,7 @@ def parse_arguments():</td>
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285
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286
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<pre style="margin: 0;"> <span id="LC286" class="line" lang="python"> <span class="s" style="color: #d14;">"""each line contains a fragment length and count. It may """</span></span>
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286
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287
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<pre style="margin: 0;"> <span id="LC287" class="line" lang="python"> <span class="p">))</span></span>
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287
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288
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<pre style="margin: 0;"> <span id="LC288" class="line" lang="python"></span>
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288
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<td class="diff-line-num new_line old" data-linenumber="289" 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="LC288" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-t'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--template-directory'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;"><span class="idiff left">locate_template_directory</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">sys</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">argv</span></span><span class="p"><span class="idiff">[</span></span><span class="mi" style="color: #099;"><span class="idiff">0</span></span><span class="p"><span class="idiff right">])</span>,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"""The location of the web app directory template."""</span><span class="p">))</span></span>
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<td class="diff-line-num new old_line" data-linenumber="289" 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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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-t'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--template-directory'</span><span class="p">,</span> <span class="n" style="color: #333;">default</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;"><span class="idiff left right">'auto'</span></span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="p">(</span><span class="s" style="color: #d14;">"""The location of the web app directory template."""</span><span class="p">))</span></span>
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289
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<td class="diff-line-num new_line" data-linenumber="290" 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">
290
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<pre style="margin: 0;"> <span id="LC290" class="line" lang="python"></span>
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290
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<td class="diff-line-num new_line" data-linenumber="291" 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">
291
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<pre style="margin: 0;"> <span id="LC291" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'-v'</span><span class="p">,</span> <span class="s" style="color: #d14;">'--verbose'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'store_true'</span><span class="p">,</span> <span class="n" style="color: #333;">help</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'Talk more.'</span><span class="p">)</span></span>
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291
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<td class="diff-line-num new_line" data-linenumber="292" 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">
292
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<pre style="margin: 0;"> <span id="LC292" class="line" lang="python"> <span class="n" style="color: #333;">parser</span><span class="p">.</span><span class="n" style="color: #333;">add_argument</span><span class="p">(</span><span class="s" style="color: #d14;">'--version'</span><span class="p">,</span> <span class="n" style="color: #333;">action</span><span class="o" style="font-weight: 600;">=</span><span class="s" style="color: #d14;">'version'</span><span class="p">,</span> <span class="n" style="color: #333;">version</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">PROGRAM_VERSION</span><span class="p">)</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="569" 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="570" 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">@@ -569,6 +570,9 @@ def write_metrics(indent, metrics):</td>
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<pre style="margin: 0;"> <span id="LC570" class="line" lang="python"><span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">__name__</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'__main__'</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC571" class="line" lang="python"> <span class="n" style="color: #333;">args</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">parse_arguments</span><span class="p">()</span></span>
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572
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<pre style="margin: 0;"> <span id="LC572" class="line" lang="python"></span>
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">template_directory</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">'auto'</span><span class="p">:</span></span>
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="python"> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">template_directory</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">locate_template_directory</span><span class="p">(</span><span class="n" style="color: #333;">sys</span><span class="p">.</span><span class="n" style="color: #333;">argv</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="LC575" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC576" class="line" lang="python"> <span class="n" style="color: #333;">loglevel</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">verbose</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">DEBUG</span> <span class="ow" style="font-weight: 600;">or</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">INFO</span></span>
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<pre style="margin: 0;"> <span id="LC577" class="line" lang="python"> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">basicConfig</span><span class="p">(</span><span class="n" style="color: #333;">level</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">loglevel</span><span class="p">,</span> <span class="nb" style="color: #0086b3;">format</span><span class="o" style="font-weight: 600;">=</span><span class="n" style="color: #333;">LOGGING_FORMAT</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC578" class="line" lang="python"> <span class="n" style="color: #333;">logger</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">logging</span><span class="p">.</span><span class="n" style="color: #333;">getLogger</span><span class="p">(</span><span class="n" style="color: #333;">PROGRAM</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">@@ -599,7 +603,7 @@ if __name__ == '__main__':</td>
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<pre style="margin: 0;"> <span id="LC603" class="line" lang="python"> <span class="n" style="color: #333;">logger</span><span class="p">.</span><span class="n" style="color: #333;">info</span><span class="p">(</span><span class="s" style="color: #d14;">'Creating data directory {}'</span><span class="p">.</span><span class="nb" style="color: #0086b3;">format</span><span class="p">(</span><span class="n" style="color: #333;">data_directory</span><span class="p">))</span></span>
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604
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<pre style="margin: 0;"> <span id="LC604" class="line" lang="python"> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">makedirs</span><span class="p">(</span><span class="n" style="color: #333;">data_directory</span><span class="p">,</span> <span class="mo" style="color: #099;">0o0755</span><span class="p">)</span></span>
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605
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<pre style="margin: 0;"> <span id="LC605" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC602" class="line" lang="python"> <span class="n" style="color: #333;">configuration</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'description'</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">description</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="s" style="color: #d14;">'metrics'</span><span class="p">:</span> <span class="p">{}}</span></span>
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="python"> <span class="n" style="color: #333;">configuration</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="s" style="color: #d14;">'description'</span><span class="p">:</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">description</span> <span class="ow" style="font-weight: 600;">or</span> <span class="s" style="color: #d14;">''</span><span class="p">,</span> <span class="s" style="color: #d14;">'metrics'</span><span class="p">:</span> <span class="p">{}<span class="idiff left">,</span></span><span class="idiff"> </span><span class="s" style="color: #d14;"><span class="idiff">'less_redundant'</span></span><span class="p"><span class="idiff">:</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">args</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">less_redundant</span></span><span class="p">}</span></span>
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607
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<pre style="margin: 0;"> <span id="LC607" class="line" lang="python"></span>
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604
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608
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<pre style="margin: 0;"> <span id="LC608" class="line" lang="python"> <span class="n" style="color: #333;">loader</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">functools</span><span class="p">.</span><span class="n" style="color: #333;">partial</span><span class="p">(</span><span class="n" style="color: #333;">load_metrics</span><span class="p">,</span> <span class="n" style="color: #333;">data_directory</span><span class="p">)</span></span>
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609
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<pre style="margin: 0;"> <span id="LC609" class="line" lang="python"> <span class="n" style="color: #333;">loaded_metrics</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">pool</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">pool</span><span class="p">.</span><span class="n" style="color: #333;">imap</span><span class="p">(</span><span class="n" style="color: #333;">loader</span><span class="p">,</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">metrics</span><span class="p">)</span> <span class="ow" style="font-weight: 600;">or</span> <span class="p">(</span><span class="n" style="color: #333;">loader</span><span class="p">(</span><span class="n" style="color: #333;">metrics_filename</span><span class="p">)</span> <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">metrics_filename</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">args</span><span class="p">.</span><span class="n" style="color: #333;">metrics</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">@@ -170,9 +170,9 @@</td>
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170
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170
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<pre style="margin: 0;"> <span id="LC170" class="line" lang="html"> <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"short_mononucleosomal_ratio"</span><span class="nt" style="color: #000080;">></span>Short-to-mononucleosomal ratio<span class="nt" style="color: #000080;"></option></span></span>
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171
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171
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<pre style="margin: 0;"> <span id="LC171" class="line" lang="html"> <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"tss_enrichment"</span><span class="nt" style="color: #000080;">></span>TSS enrichment<span class="nt" style="color: #000080;"></option></span></span>
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172
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<td class="diff-line-num new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="html"> <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"max_fraction_reads_from_single_autosome"</span><span class="nt" style="color: #000080;">></span>Maximum fraction of reads from a single autosome<span class="nt" style="color: #000080;"></option></span></span>
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173
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<pre style="margin: 0;">-<span id="LC173" class="line" lang="html"> <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"duplicate_fraction_in_peaks"</span><span class="nt" style="color: #000080;">></span>Duplicate fraction in peaks<span class="nt" style="color: #000080;"></option></span></span>
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174
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<td class="diff-line-num new_line old" data-linenumber="173" 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="LC174" class="line" lang="html"> <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"duplicate_fraction_not_in_peaks"</span><span class="nt" style="color: #000080;">></span>Duplicate fraction outside of peaks<span class="nt" style="color: #000080;"></option></span></span>
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175
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<td class="diff-line-num new_line old" data-linenumber="173" 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="LC175" class="line" lang="html"> <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"peak_duplicate_ratio"</span><span class="nt" style="color: #000080;">></span>Peak duplicate ratio<span class="nt" style="color: #000080;"></option></span></span>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="html"> <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"duplicate_fraction_in_peaks"</span><span class="nt" style="color: #000080;">></span>Duplicate fraction in peaks<span class="nt" style="color: #000080;"></option></span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="html"> <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"duplicate_fraction_not_in_peaks"</span><span class="nt" style="color: #000080;">></span>Duplicate fraction outside of peaks<span class="nt" style="color: #000080;"></option></span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="html"> <span class="nt" style="color: #000080;"><option</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">value=</span><span class="s" style="color: #d14;">"peak_duplicate_ratio"</span><span class="nt" style="color: #000080;">></span>Peak duplicate ratio<span class="nt" style="color: #000080;"></option></span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="html"> <span class="nt" style="color: #000080;"></select></span></span>
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="html"> <span class="nt" style="color: #000080;"></label></span></span>
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="html"> <span class="nt" style="color: #000080;"></div></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">@@ -349,16 +349,16 @@</td>
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349
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<pre style="margin: 0;"> <span id="LC349" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"max_fraction_reads_from_single_autosome"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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350
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<td class="diff-line-num new_line" data-linenumber="350" 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">
350
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<pre style="margin: 0;"> <span id="LC350" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The fraction of HQAA reads derived from the autosome with the greatest number of HQAA reads. Ideally, this should be approximately equal to the length of the longest autosome divided by the summed length of all autosomes. Outliers in this metric may reflect abnormal karyotypes or, in the case of single-cell/single-nucleus data, it may indicate that DNA from another source is being assigned to that cell/nucleus."</span><span class="nt" style="color: #000080;">></span>Max. fraction HQAA from one autosome<span class="nt" style="color: #000080;"></span></span></span>
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351
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351
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<pre style="margin: 0;"> <span id="LC351" class="line" lang="html"> <span class="nt" style="color: #000080;"></th></span></span>
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352
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<pre style="margin: 0;">-<span id="LC352" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"duplicate_fraction_in_peaks"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"duplicate_fraction_in_peaks"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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353
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<td class="diff-line-num new_line" data-linenumber="353" 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">
353
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<pre style="margin: 0;"> <span id="LC353" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The fraction of properly paired reads that mapped within peaks and were marked as duplicates."</span><span class="nt" style="color: #000080;">></span>Duplicate fraction in peaks<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;"> <span id="LC354" class="line" lang="html"> <span class="nt" style="color: #000080;"></th></span></span>
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<pre style="margin: 0;">-<span id="LC356" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"duplicate_fraction_not_in_peaks"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"duplicate_fraction_not_in_peaks"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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357
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<pre style="margin: 0;"> <span id="LC357" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The fraction of properly paired reads that mapped outside of peaks and were marked as duplicates."</span><span class="nt" style="color: #000080;">></span>Duplicate fraction outside of peaks<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;">-<span id="LC360" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"peak_duplicate_ratio"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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361
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<td class="diff-line-num new_line old" data-linenumber="360" 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="LC361" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The ratio of the fraction of properly paired reads that mapped outside of peaks and were marked as duplicates to the fraction of properly paired reads that mapped within peaks and were marked as duplicates."</span><span class="nt" style="color: #000080;">></span>Peak duplicate ratio<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"peak_duplicate_ratio"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The ratio of the fraction of properly paired reads that mapped outside of peaks and were marked as duplicates to the fraction of properly paired reads that mapped within peaks and were marked as duplicates."</span><span class="nt" style="color: #000080;">></span>Peak duplicate ratio<span class="nt" style="color: #000080;"></span></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">@@ -396,10 +396,10 @@</td>
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<pre style="margin: 0;"> <span id="LC396" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.duplicate_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC397" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"Duplicate alignments as a percentage of total reads."</span><span class="nt" style="color: #000080;">></span>Duplicate<span class="ni" style="color: #800080;"> </span>(%)<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;"> <span id="LC398" class="line" lang="html"> <span class="nt" style="color: #000080;"></th></span></span>
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<pre style="margin: 0;">-<span id="LC399" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"mean_mapq"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"mean_mapq"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC400" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The mean mapping quality of the experiment's reads."</span><span class="nt" style="color: #000080;">></span>Mean mapping quality<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;"> <span id="LC401" class="line" lang="html"> <span class="nt" style="color: #000080;"></th></span></span>
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<pre style="margin: 0;">-<span id="LC402" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"median_mapq"</span> <span class="na" style="color: #008080;">data-metrictype=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"median_mapq"</span> <span class="na" style="color: #008080;">data-metrictype=</span><span class="s" style="color: #d14;">"integer"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC403" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The median mapping quality of the experiment's reads."</span><span class="nt" style="color: #000080;">></span>Median mapping quality<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;">-<span id="LC466" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.rf_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.rf_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC467" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"for-export"</span><span class="nt" style="color: #000080;">></span>Of all reads, the percentage that paired and mapped but <span class="nt" style="color: #000080;"></span><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The reads of a proper pair should point toward each other, with the end mapped to the smaller coordinate on the forward strand and the other end on the reverse strand -- FR orientation. These reads were in pairs oriented RF, where the smaller coordinate was on the reverse strand and the larger on the forward strand."</span><span class="nt" style="color: #000080;">></span>RF<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;">-<span id="LC469" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.ff_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.ff_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC470" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"for-export"</span><span class="nt" style="color: #000080;">></span>Of all reads, the percentage that paired and mapped but <span class="nt" style="color: #000080;"></span><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The reads of a proper pair should point toward each other, with the end mapped to the smaller coordinate on the forward strand and the other end on the reverse strand -- FR orientation. These reads were in pairs oriented FF, where both reads mapped on the forward strand."</span><span class="nt" style="color: #000080;">></span>FF<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;">-<span id="LC472" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.rr_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.rr_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC473" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"for-export"</span><span class="nt" style="color: #000080;">></span>Of all reads, the percentage that paired and mapped but <span class="nt" style="color: #000080;"></span><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The reads of a proper pair should point toward each other, with the end mapped to the smaller coordinate on the forward strand and the other end on the reverse strand -- FR orientation. These reads were in pairs oriented RR, where both reads mapped on the reverse strand."</span><span class="nt" style="color: #000080;">></span>RR<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;"> <span id="LC475" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.reads_with_mate_mapped_to_different_reference__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">-<span id="LC510" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.total_autosomal_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.total_autosomal_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC511" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"for-export"</span><span class="nt" style="color: #000080;">></span>Autosomal, <span class="nt" style="color: #000080;"></span><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The number of reads aligned to autosomes, as a percentage of all reads."</span><span class="nt" style="color: #000080;">></span>% of all reads<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;"> <span id="LC513" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.duplicate_autosomal_reads__total_autosomal_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC516" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.total_mitochondrial_reads__total_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC517" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"for-export"</span><span class="nt" style="color: #000080;">></span>Mitochondrial, <span class="nt" style="color: #000080;"></span><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The number of reads aligned to the mitochondrial reference, as a percentage of all reads."</span><span class="nt" style="color: #000080;">></span>% of all reads<span class="nt" style="color: #000080;"></span></span></span>
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<pre style="margin: 0;">-<span id="LC519" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.duplicate_mitochondrial_reads__total_mitochondrial_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="html"> <span class="nt" style="color: #000080;"><th</span> <span class="na" style="color: #008080;"><span class="idiff left">class=</span></span><span class="s" style="color: #d14;"><span class="idiff">"redundant"</span></span><span class="idiff right"> </span><span class="na" style="color: #008080;">data-metric=</span><span class="s" style="color: #d14;">"percentages.duplicate_mitochondrial_reads__total_mitochondrial_reads"</span> <span class="na" style="color: #008080;">data-priority=</span><span class="s" style="color: #d14;">"1"</span><span class="nt" style="color: #000080;">></span></span>
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<pre style="margin: 0;"> <span id="LC520" class="line" lang="html"> <span class="nt" style="color: #000080;"><span</span> <span class="na" style="color: #008080;">class=</span><span class="s" style="color: #d14;">"for-export"</span><span class="nt" style="color: #000080;">></span>Mitochondrial, <span class="nt" style="color: #000080;"></span><span</span> <span class="na" style="color: #008080;">data-hovertext=</span><span class="s" style="color: #d14;">"The percentage of reads mapped to the mitochondrial reference that were duplicates."</span><span class="nt" style="color: #000080;">></span>Duplicates<span class="ni" style="color: #800080;"> </span>(% of mitochondrial alignments)<span class="nt" style="color: #000080;"></span></span></span>
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<a href="https://salsa.debian.org/med-team/ataqv/-/commit/7e5d52302338e2326b96c34d7da88ac8da3594df#3d6e52c1c03d213496ef289d51d3aa940e4de480"><strong>src/web/js/ataqv.js</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">@@ -1588,6 +1588,9 @@ let ataqv = (function() {</td>
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<pre style="margin: 0;"> <span id="LC1589" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="kd" style="font-weight: 600;">let</span> <span class="nx">headerCell</span> <span class="k" style="font-weight: 600;">of</span> <span class="nx">querySelectorAll</span><span class="p">([</span><span class="dl">'</span><span class="s1" style="color: #d14;">th[data-metric]</span><span class="dl">'</span><span class="p">],</span> <span class="nx">table</span><span class="p">))</span> <span class="p">{</span></span>
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1590
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1590
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<pre style="margin: 0;"> <span id="LC1590" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">let</span> <span class="nx">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="nx">headerCell</span><span class="p">.</span><span class="nx">dataset</span><span class="p">.</span><span class="nx">metric</span><span class="p">;</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1591" 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="diff-line-num new new_line" data-linenumber="1591" 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">
1591
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<pre style="margin: 0;">+<span id="LC1591" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">configuration</span><span class="p">.</span><span class="nx">less_redundant</span> <span class="o" style="font-weight: 600;">&&</span> <span class="nx">headerCell</span><span class="p">.</span><span class="nx">className</span> <span class="o" style="font-weight: 600;">==</span> <span class="dl">'</span><span class="s1" style="color: #d14;">redundant</span><span class="dl">'</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1592" 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">
1592
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<pre style="margin: 0;">+<span id="LC1592" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">continue</span><span class="p">;</span></span>
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1593
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<pre style="margin: 0;">+<span id="LC1593" class="line" lang="javascript"> <span class="p">}</span></span>
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1591
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<td class="diff-line-num new_line" data-linenumber="1594" 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">
1594
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<pre style="margin: 0;"> <span id="LC1594" class="line" lang="javascript"> <span class="nx">keys</span><span class="p">.</span><span class="nx">push</span><span class="p">(</span><span class="nx">key</span><span class="p">);</span></span>
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1592
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1595
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<pre style="margin: 0;"> <span id="LC1595" class="line" lang="javascript"></span>
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1593
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1596
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<pre style="margin: 0;"> <span id="LC1596" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">let</span> <span class="nx">col</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="1831" 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="1834" 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">@@ -1831,6 +1834,11 @@ let ataqv = (function() {</td>
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1831
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1834
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<pre style="margin: 0;"> <span id="LC1834" class="line" lang="javascript"> <span class="p">}</span></span>
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<td class="diff-line-num old_line" data-linenumber="1832" 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">
1832
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<td class="diff-line-num new_line" data-linenumber="1835" 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">
1835
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<pre style="margin: 0;"> <span id="LC1835" class="line" lang="javascript"></span>
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<td class="diff-line-num old_line" data-linenumber="1833" 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">
1833
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<td class="diff-line-num new_line" data-linenumber="1836" 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">
1836
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<pre style="margin: 0;"> <span id="LC1836" class="line" lang="javascript"> <span class="nx">loadExperiments</span><span class="p">();</span></span>
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<td class="diff-line-num new old_line" data-linenumber="1834" 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="diff-line-num new new_line" data-linenumber="1837" 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">
1837
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<pre style="margin: 0;">+<span id="LC1837" class="line" lang="javascript"></span>
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<td class="diff-line-num new new_line" data-linenumber="1838" 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">
1838
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<pre style="margin: 0;">+<span id="LC1838" class="line" lang="javascript"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nx">configuration</span><span class="p">.</span><span class="nx">less_redundant</span><span class="p">)</span> <span class="p">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1839" 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">
1839
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<pre style="margin: 0;">+<span id="LC1839" class="line" lang="javascript"> <span class="nx">d3</span><span class="p">.</span><span class="nx">selectAll</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">.redundant</span><span class="dl">'</span><span class="p">).</span><span class="nx">style</span><span class="p">(</span><span class="dl">"</span><span class="s2" style="color: #d14;">display</span><span class="dl">"</span><span class="p">,</span> <span class="dl">"</span><span class="s2" style="color: #d14;">none</span><span class="dl">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1840" 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">
1840
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<pre style="margin: 0;">+<span id="LC1840" class="line" lang="javascript"> <span class="nx">$</span><span class="p">(</span><span class="dl">'</span><span class="s1" style="color: #d14;">[colspan=2]</span><span class="dl">'</span><span class="p">).</span><span class="nx">attr</span><span class="p">(</span><span class="dl">"</span><span class="s2" style="color: #d14;">colspan</span><span class="dl">"</span><span class="p">,</span> <span class="dl">"</span><span class="s2" style="color: #d14;">1</span><span class="dl">"</span><span class="p">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="1841" 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">
1841
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<pre style="margin: 0;">+<span id="LC1841" class="line" lang="javascript"> <span class="p">}</span></span>
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1834
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1842
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<pre style="margin: 0;"> <span id="LC1842" class="line" lang="javascript"> <span class="p">}</span></span>
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1835
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<td class="diff-line-num new_line" data-linenumber="1843" 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">
1843
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<pre style="margin: 0;"> <span id="LC1843" class="line" lang="javascript"></span>
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1836
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<td class="diff-line-num new_line" data-linenumber="1844" 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">
1844
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<pre style="margin: 0;"> <span id="LC1844" class="line" lang="javascript"> <span class="kd" style="font-weight: 600;">function</span> <span class="nx">configure</span><span class="p">(</span><span class="nx">conf</span><span class="p">)</span> <span class="p">{</span></span>
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