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GitLab

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<h3>

Steffen Möller pushed to branch upstream

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd">4737abe3</a></strong>

<div>

<span>by Steffen Moeller</span>

<i>at 2019-12-21T18:10:21Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.3</pre>

</li>

</ul>

<h4>15 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">

.travis.yml

</a>

</li>

<li class="file-stats">

<a href="#8b020ecbc6060870763ef64017f02bc5d900838f">

docs/source/_static/nanopolish-workflow.png

</a>

</li>

<li class="file-stats">

<a href="#25a119345b2ab98afec596f84420ea5ab628a3c1">

docs/source/quickstart_call_methylation.rst

</a>

</li>

<li class="file-stats">

<a href="#b533e7cbb3f06e3619863bd2a00e4f83882b3c8e">

docs/source/quickstart_polya.rst

</a>

</li>

<li class="file-stats">

<a href="#a179b8d0065d58637970381d3ea01facee70712c">

scripts/convert_all_models.py

</a>

</li>

<li class="file-stats">

<a href="#60a5721c894e842dc781381835d1997600ec9cd6">

scripts/import_ont_model.py

</a>

</li>

<li class="file-stats">

<a href="#dae6e97a9a46a6a65d45ce6275cc6e9424e0077f">

scripts/nanopolish_merge.py

</a>

</li>

<li class="file-stats">

<a href="#accc6e1bf582ffda3d446f39c6d88187711ded9a">

scripts/polya_training/dump_signal.py

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<li class="file-stats">

<a href="#d20492b3a0e27e63052ed471166cee57a40c5cb9">

scripts/polya_training/hmmplot.py

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<a href="#a533feab8d3540e053620be917dd5fbf533458b2">

scripts/polya_training/retrain_emission.py

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<a href="#30f30a527501f95bc409aa2919835ea54b6e1bba">

scripts/reestimate_polya_emissions.py

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<li class="file-stats">

<a href="#58a43c64ead5187f569b28ec5ca98b313c48d7c7">

src/common/nanopolish_common.h

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<li class="file-stats">

<a href="#2d62e059707d17d6d88d86a4af4fce9c4c482e3d">

src/nanopolish_index.cpp

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<li class="file-stats">

<a href="#ecc53e18e8deb4dabc0e2ec2afe10d1d4c114f91">

src/nanopolish_phase_reads.cpp

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<li class="file-stats">

<a href="#8a4594db09bdbd5859ea2b82ef08bae7e6cb4eba">

src/nanopolish_vcf2fasta.cpp

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</ul>

<h4>Changes:</h4>

<li id="dea01dd89a3b602828e630677fde5d77c06441c8">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#dea01dd89a3b602828e630677fde5d77c06441c8"><strong>.travis.yml</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># travis.yml for github.com/jts/nanopolish</span></span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC4" class="line" lang="yaml"><span class="na" style="color: #008080;">services</span><span class="pi">:</span> <span class="s" style="color: #d14;">docker</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="yaml"><span class="na" style="color: #008080;">language</span><span class="pi">:</span> <span class="s" style="color: #d14;">generic</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="yaml"><span class="na" style="color: #008080;">cache</span><span class="pi">:</span> <span class="s" style="color: #d14;">apt</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">git</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC9" class="line" lang="yaml">    <span class="na" style="color: #008080;">depth</span><span class="pi">:</span> <span class="m" style="color: #099;">1</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="yaml"><span class="s" style="color: #d14;">.nanopolish.ci.matrix-definitions</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml">    <span class="pi">-</span> <span class="nl">&cron-only</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml">      <span class="na" style="color: #008080;">if</span><span class="pi">:</span> <span class="s" style="color: #d14;">type = cron OR env(CI_CRON) = </span><span class="no" style="color: #008080;">true</span></span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml">    <span class="pi">-</span> <span class="nl">&arch</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml">      <span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml">          <span class="pi">-</span> <span class="pi">|</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml">            <span class="s" style="color: #d14;">sed -i "/^FROM / s/arm64/${ARCH}/" Dockerfile-arm</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml">          <span class="pi">-</span> <span class="pi">|</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml">            <span class="s" style="color: #d14;">docker run --rm --privileged \</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml">                <span class="s" style="color: #d14;">multiarch/qemu-user-static:register --reset && \</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml">                <span class="s" style="color: #d14;">docker build --rm -t nanopolish -f Dockerfile-arm .</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml">      <span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml">          <span class="pi">-</span> <span class="pi">|</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml">            <span class="s" style="color: #d14;">docker run --rm -t \</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="yaml">                <span class="s" style="color: #d14;">-e HDF5="${HDF5:-install}" \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="yaml">                <span class="s" style="color: #d14;">-e H5_CFLAGS="${H5_CFLAGS}" \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="yaml">                <span class="s" style="color: #d14;">-e HDF5_VERSION="1.10.4" \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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="LC28" class="line" lang="yaml">                <span class="s" style="color: #d14;">-e H5_INCLUDE="${H5_INCLUDE}" \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" 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="LC29" class="line" lang="yaml">                <span class="s" style="color: #d14;">-e LDFLAGS="${LDFLAGS}" \</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="4" 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="LC30" class="line" lang="yaml">                <span class="s" style="color: #d14;">nanopolish</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="31" 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="LC4" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" 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="LC33" class="line" lang="yaml">    <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" 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="LC34" class="line" lang="yaml">        <span class="c1" style="color: #998; font-style: italic;"># Set env for both nanoplish and the dependency hdf5.</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="35" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC35" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="36" 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="LC36" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">CC=gcc-4.8</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC37" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">CXX=g++-4.8</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC38" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">AR=gcc-ar-4.8</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="39" 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="LC39" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">NM=gcc-nm-4.8</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="40" 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="LC40" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">RANLIB=gcc-ranlib-4.8</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="41" 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="LC41" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="42" 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="LC42" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">CC=gcc-8</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="43" 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="LC43" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">CXX=g++-8</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="44" 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="LC44" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">AR=gcc-ar-8</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="45" 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="LC45" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">NM=gcc-nm-8</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="46" 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="LC46" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">RANLIB=gcc-ranlib-8</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="47" 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="LC47" class="line" lang="yaml">        <span class="c1" style="color: #998; font-style: italic;"># aarch64 - ARM 64-bit</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="48" 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="LC48" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">aarch64</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="49" 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="LC49" class="line" lang="yaml">          <span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="s" style="color: #d14;">required</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="50" 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="LC50" class="line" lang="yaml">          <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="51" 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="LC51" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">ARCH=arm64</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" 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="LC52" class="line" lang="yaml">          <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*arch</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="53" 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="LC53" class="line" lang="yaml">          <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*cron-only</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="54" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">aarch64-system-hdf5</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="55" 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="LC55" class="line" lang="yaml">          <span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="s" style="color: #d14;">required</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="56" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="yaml">          <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="57" 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="LC57" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">ARCH=arm64</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">HDF5="system"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">H5_INCLUDE="-I/usr/include/hdf5/serial"</span></span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">LDFLAGS="-L/usr/lib/aarch64-linux-gnu/hdf5/serial"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="yaml">          <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*arch</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="yaml">        <span class="c1" style="color: #998; font-style: italic;"># armv7l - ARM 32-bit</span></span>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">armv7l</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="yaml">          <span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="s" style="color: #d14;">required</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="yaml">          <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">ARCH=armhf</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="yaml">          <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*arch</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="yaml">          <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*cron-only</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">armv7l-system-hdf5</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="yaml">          <span class="na" style="color: #008080;">sudo</span><span class="pi">:</span> <span class="s" style="color: #d14;">required</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="yaml">          <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">ARCH=armhf</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">HDF5="system"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">H5_INCLUDE="-I/usr/include/hdf5/serial"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="yaml">              <span class="pi">-</span> <span class="s" style="color: #d14;">LDFLAGS="-L/usr/lib/arm-linux-gnueabihf/hdf5/serial"</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC76" class="line" lang="yaml">          <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*arch</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC77" class="line" lang="yaml">    <span class="na" style="color: #008080;">allow_failures</span><span class="pi">:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="yaml">        <span class="c1" style="color: #998; font-style: italic;"># The jobs installing hdf5 from source in docker finishes with error</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="79" 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="LC79" class="line" lang="yaml">        <span class="c1" style="color: #998; font-style: italic;"># because of the job exceeded the maximum time limit (50 minutes).</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">aarch64</span></span>

</pre>

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81

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="yaml">        <span class="pi">-</span> <span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">armv7l</span></span>

</pre>

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82

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="83" 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="LC83" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Install and export newer gcc</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="84" 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="LC84" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="85" 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="LC85" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="86" 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="LC86" class="line" lang="yaml">    <span class="pi">-</span> <span class="s" style="color: #d14;">sudo apt-get update -qq</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="87" 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="LC87" class="line" lang="yaml">    <span class="pi">-</span> <span class="pi">|</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="88" 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="LC88" class="line" lang="yaml">      <span class="s" style="color: #d14;">if [[ "${CC}" =~ ^gcc- ]]; then</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="89" 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="LC89" class="line" lang="yaml">          <span class="s" style="color: #d14;">echo "Installing ${CC}."</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="90" 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="LC90" class="line" lang="yaml">          <span class="s" style="color: #d14;">sudo apt-get install -qq "${CC}"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="91" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC91" class="line" lang="yaml">      <span class="s" style="color: #d14;">fi</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="92" 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="LC92" class="line" lang="yaml">    <span class="pi">-</span> <span class="pi">|</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="93" 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="LC93" class="line" lang="yaml">      <span class="s" style="color: #d14;">if [[ "${CXX}" =~ ^g\+\+- ]]; then</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="94" 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="LC94" class="line" lang="yaml">          <span class="s" style="color: #d14;">echo "Installing ${CXX}."</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="95" 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="LC95" class="line" lang="yaml">          <span class="s" style="color: #d14;">sudo apt-get install -qq "${CXX}"</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="96" 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="LC96" class="line" lang="yaml">      <span class="s" style="color: #d14;">fi</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="yaml">  <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

8

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="yaml">      <span class="na" style="color: #008080;">arch</span><span class="pi">:</span> <span class="s" style="color: #d14;">amd64</span></span>

</pre>

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

9

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

<pre style="margin: 0;">+<span id="LC9" class="line" lang="yaml">      <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="yaml">        <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

11

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="yaml">          <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

12

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="13" 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">

13

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="yaml">          <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="14" 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">

14

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">g++-4.9</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="15" 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">

15

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="yaml">      <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">CC=gcc-4.9</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">CXX=g++-4.9</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">AR=gcc-ar-4.9</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">NM=gcc-nm-4.9</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">RANLIB=gcc-ranlib-4.9"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="16" 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">

16

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

<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

17

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

<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml">      <span class="na" style="color: #008080;">arch</span><span class="pi">:</span> <span class="s" style="color: #d14;">amd64</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

18

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

<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml">      <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

19

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

<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml">        <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

20

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

<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml">          <span class="na" style="color: #008080;">sources</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

21

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">ubuntu-toolchain-r-test</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

22

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="yaml">          <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

23

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">g++-8</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

24

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml">      <span class="na" style="color: #008080;">env</span><span class="pi">:</span> <span class="s2" style="color: #d14;">"</span><span class="s" style="color: #d14;">CC=gcc-8</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">CXX=g++-8</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">AR=gcc-ar-8</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">NM=gcc-nm-8</span><span class="nv" style="color: #008080;"> </span><span class="s" style="color: #d14;">RANLIB=gcc-ranlib-8"</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

25

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

<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml">    <span class="pi">-</span> <span class="na" style="color: #008080;">os</span><span class="pi">:</span> <span class="s" style="color: #d14;">linux</span></span>

</pre>

</td>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml">      <span class="na" style="color: #008080;">arch</span><span class="pi">:</span> <span class="s" style="color: #d14;">arm64</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

27

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml">      <span class="na" style="color: #008080;">addons</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml">        <span class="na" style="color: #008080;">apt</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="29" 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">

29

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml">          <span class="na" style="color: #008080;">packages</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="30" 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="LC30" class="line" lang="yaml">            <span class="pi">-</span> <span class="s" style="color: #d14;">libhdf5-serial-dev</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="31" 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="LC31" class="line" lang="yaml">      <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="32" 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="LC32" class="line" lang="yaml">        <span class="pi">-</span> <span class="s" style="color: #d14;">HDF5="system"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="33" 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="LC33" class="line" lang="yaml">        <span class="pi">-</span> <span class="s" style="color: #d14;">H5_INCLUDE="-I/usr/include/hdf5/serial"</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="yaml">        <span class="pi">-</span> <span class="s" style="color: #d14;">LDFLAGS="-L/usr/lib/aarch64-linux-gnu/hdf5/serial"</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="35" 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="LC35" class="line" lang="yaml"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" 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="LC36" class="line" lang="yaml"><span class="na" style="color: #008080;">before_script</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" 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="LC37" class="line" lang="yaml">    <span class="c1" style="color: #998; font-style: italic;"># Suppress all compiler warnings for hdf5 Makefile</span></span>

</pre>

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<br>

</li>

<li id="8b020ecbc6060870763ef64017f02bc5d900838f">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#8b020ecbc6060870763ef64017f02bc5d900838f"><strong>docs/source/_static/nanopolish-workflow.png</strong></a>

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<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#25a119345b2ab98afec596f84420ea5ab628a3c1"><strong>docs/source/quickstart_call_methylation.rst</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ In this tutorial we will use a subset of the `NA12878 WGS Consortium data <https</td>

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27

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<td class="diff-line-num new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

29

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<td class="diff-line-num new_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">* Sample :   Human cell line (NA12878)</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="30" 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="LC30" class="line" lang="plaintext">* Basecaller : <span class="idiff left right">Albacore v2.0.2</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="30" 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">

30

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">* Basecaller : <span class="idiff left right">Guppy v2.3.5</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="31" 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="LC31" class="line" lang="plaintext">* Region: chr20:5,000,000-10,000,000</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="32" 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="LC32" class="line" lang="plaintext"></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">In the extracted example data you should find the following files:</span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="38" 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="38" 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">@@ -38,35 +38,35 @@ In the extracted example data you should find the following files:</td>

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<td class="diff-line-num old_line" data-linenumber="38" 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="LC38" class="line" lang="plaintext"></span>

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<td class="diff-line-num old_line" data-linenumber="39" 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="LC39" class="line" lang="plaintext">The reads were basecalled using this albacore command: ::</span>

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<td class="diff-line-num old_line" data-linenumber="40" 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="LC40" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="plaintext">    <span class="idiff left right">read_fast5_basecaller.py -c r94_450bps_linear.cfg -t 8 -i fast5_files -s basecalled/ -o fastq</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="42" 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="LC41" class="line" lang="plaintext">    <span class="idiff left right">guppy_basecaller -c dna_r9.4.1_450bps_flipflop.cfg -i fast5_files/ -s basecalled/</span></span>

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<td class="diff-line-num old_line" data-linenumber="42" 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="LC42" class="line" lang="plaintext"></span>

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<td class="diff-line-num old_line" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="43" 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="LC43" class="line" lang="plaintext">After the basecaller finished, we merged all of the fastq files together into a single file: ::</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="44" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="44" 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="LC44" class="line" lang="plaintext"></span>

</pre>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="plaintext">    cat basecalled/<span class="idiff left right">workspace/pass/*.fastq > albacore_</span>output.fastq</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="46" 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="LC45" class="line" lang="plaintext">    cat basecalled/<span class="idiff left right">*.fastq > </span>output.fastq</span>

</pre>

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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="47" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="47" 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="LC47" class="line" lang="plaintext">Data preprocessing</span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="48" 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="LC48" class="line" lang="plaintext">------------------------------------</span>

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<td class="diff-line-num old_line" data-linenumber="49" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="49" 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="LC49" class="line" lang="plaintext"></span>

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<td class="diff-line-num old_line" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="50" 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="LC50" class="line" lang="plaintext">nanopolish needs access to the signal-level data measured by the nanopore sequencer. To begin, we need to create an index file that links read ids with their signal-level data in the FAST5 files: ::</span>

</pre>

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="52" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="52" 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="LC52" class="line" lang="plaintext">    nanopolish index -d fast5_files/ <span class="idiff left right">albacore_</span>output.fastq</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="53" 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="52" 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="LC52" class="line" lang="plaintext">    nanopolish index -d fast5_files/ output.fastq</span>

</pre>

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

</pre>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="plaintext">We get the following files: ``<span class="idiff left right">albacore_output.fastq.index``, ``albacore_output.fastq.index.fai``, ``albacore_output.fastq.index.gzi``, and ``albacore_</span>output.fastq.index.readdb``.</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="55" 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="54" 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="LC54" class="line" lang="plaintext">We get the following files: ``<span class="idiff left right">output.fastq.index``, ``output.fastq.index.fai``, ``output.fastq.fastq.index.gzi``, and ``</span>output.fastq.index.readdb``.</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="55" 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">

55

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<td class="diff-line-num new_line" data-linenumber="55" 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">

55

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="56" 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">

56

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<td class="diff-line-num new_line" data-linenumber="56" 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">

56

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<pre style="margin: 0;"> <span id="LC56" class="line" lang="plaintext">Aligning reads to the reference genome</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="57" 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">

57

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<td class="diff-line-num new_line" data-linenumber="57" 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="LC57" class="line" lang="plaintext">--------------------------------------</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="58" 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="LC58" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" 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">

59

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<td class="diff-line-num new_line" data-linenumber="59" 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="LC59" class="line" lang="plaintext">Next, we need to align the basecalled reads to the reference genome. We use minimap2 as it is fast enough to map reads to the human genome. In this example we'll pipe the output directly into ``samtools sort`` to get a sorted bam file: ::</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="60" 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">

60

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<td class="diff-line-num new_line" data-linenumber="60" 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="LC60" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="plaintext">    minimap2 -a -x map-ont reference.fasta <span class="idiff left right">albacore_output.fastq | samtools sort -T tmp -o albacore_</span>output.sorted.bam</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="62" 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">

62

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<td class="diff-line-num new_line old" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="plaintext">    samtools index <span class="idiff left right">albacore_</span>output.sorted.bam</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" 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="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">    minimap2 -a -x map-ont reference.fasta <span class="idiff left right">output.fastq | samtools sort -T tmp -o </span>output.sorted.bam</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="62" 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="LC62" class="line" lang="plaintext">    samtools index output.sorted.bam</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="64" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="64" 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="LC64" class="line" lang="plaintext">Calling methylation</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="65" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="66" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="67" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="67" 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="LC67" class="line" lang="plaintext">Now we're ready to use nanopolish to detect methylated bases (in this case 5-methylcytosine in a CpG context). The command is fairly straightforward - we have to tell it what reads to use (``<span class="idiff left right">albacore_output.fastq``), where the alignments are (``albacore_</span>output.sorted.bam``), the reference genome (``reference.fasta``) and what region of the genome we're interested in (``chr20:5,000,000-10,000,000``)::</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="68" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="67" 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="LC67" class="line" lang="plaintext">Now we're ready to use nanopolish to detect methylated bases (in this case 5-methylcytosine in a CpG context). The command is fairly straightforward - we have to tell it what reads to use (``<span class="idiff left right">output.fastq``), where the alignments are (``</span>output.sorted.bam``), the reference genome (``reference.fasta``) and what region of the genome we're interested in (``chr20:5,000,000-10,000,000``)::</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="68" 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">

68

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<td class="diff-line-num new_line" data-linenumber="68" 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="LC68" class="line" lang="plaintext">     </span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="69" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="69" 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="LC69" class="line" lang="plaintext">    nanopolish call-methylation -t 8 -r <span class="idiff left right">albacore_output.fastq -b albacore_</span>output.sorted.bam -g reference.fasta -w "chr20:5,000,000-10,000,000" > methylation_calls.tsv</span>

</pre>

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</td>

<td class="diff-line-num new new_line" data-linenumber="69" 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="LC69" class="line" lang="plaintext">    nanopolish call-methylation -t 8 -r <span class="idiff left right">output.fastq -b </span>output.sorted.bam -g reference.fasta -w "chr20:5,000,000-10,000,000" > methylation_calls.tsv</span>

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

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<pre style="margin: 0;"> <span id="LC71" class="line" lang="plaintext">The output file contains a lot of information including the position of the CG dinucleotide on the reference genome, the ID of the read that was used to make the call, and the log-likelihood ratio calculated by our model: ::</span>

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

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<br>

</li>

<li id="b533e7cbb3f06e3619863bd2a00e4f83882b3c8e">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#b533e7cbb3f06e3619863bd2a00e4f83882b3c8e"><strong>docs/source/quickstart_polya.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">@@ -23,8 +23,8 @@ Let's start by downloading a dataset of fast5 files from the European Nucleotide</td>

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">    mkdir data && mkdir data/fastqs</span>

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">    wget ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR276/ERR2764784/30xpolyA.tar.gz -O 30xpolyA.tar.gz && mv 30xpolyA.tar.gz data/</span>

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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">    tar -xzf data/30xpolyA.tar.gz -C data/</span>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">    <span class="idiff left right">read_fast5_basecaller.py --worker_threads=8 -f FLO-MIN107 -k SQK-RNA001 -q 0 -s data/fastqs -i data/30xpolyA/fast5/pas</span>s</span>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext">    cat data/fastqs/<span class="idiff left right">workspace/pass/</span>*.fastq > data/30xpolyA.fastq</span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">    <span class="idiff left right">guppy_basecaller -c rna_r9.4.1_70bps_hac.cfg -i data/30xpolyA/fast5/pass -s data/fastq</span>s</span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">    cat data/fastqs/*.fastq > data/30xpolyA.fastq</span>

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

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<pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">In the above, change the value of the `-f` and `-k` arguments based on your flow-cell and sequencing kit, as the basecaller's accuracy is highly dependent upon these settings.</span>

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<pre style="margin: 0;"> <span id="LC30" 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">@@ -57,7 +57,7 @@ Align with minimap2 and format the BAM file</td>

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext">Now we'll align our basecalled mRNA sequences in the fastq file with our reference. First download a reference fasta: ::</span>

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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"></span>

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<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext">    wget https://raw.githubusercontent.com/paultsw/polya_analysis/master/data/references/enolase_reference.fas</span>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="plaintext">    wget https://raw.githubusercontent.com/paultsw/polya_analysis/master/data/references/enolase_reference.fai</span>

</pre>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">    wget https://raw.githubusercontent.com/paultsw/polya_analysis/master/data/references/enolase_reference.fa<span class="idiff left right">s.fa</span>i</span>

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61

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<td class="diff-line-num new_line" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext">    mv enolase_reference.* data/</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

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<td class="diff-line-num new_line" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

62

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

63

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<td class="diff-line-num new_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext">Note that our directory structure should now look like this: ::</span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="a179b8d0065d58637970381d3ea01facee70712c">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#a179b8d0065d58637970381d3ea01facee70712c"><strong>scripts/convert_all_models.py</strong></a>

<hr>

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

</td>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python3</span></span>

</pre>

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1

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<td class="diff-line-num 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">

2

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

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

</pre>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="60a5721c894e842dc781381835d1997600ec9cd6">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#60a5721c894e842dc781381835d1997600ec9cd6"><strong>scripts/import_ont_model.py</strong></a>

<hr>

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1

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<td class="diff-line-num new_line old" data-linenumber="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/<span class="idiff left right">python</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="2" 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="1" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/<span class="idiff left right">env python3</span></span></span>

</pre>

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<td class="diff-line-num old_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">

2

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<td class="diff-line-num 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">

2

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># This script takes a .model file provided by ONT and adds metadata that allows it</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># to be compiled into nanopolish</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="dae6e97a9a46a6a65d45ce6275cc6e9424e0077f">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#dae6e97a9a46a6a65d45ce6275cc6e9424e0077f"><strong>scripts/nanopolish_merge.py</strong></a>

<hr>

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</td>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python3</span></span>

</pre>

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1

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<td class="diff-line-num 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">

2

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

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

</pre>

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<td class="diff-line-num old_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">

2

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

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

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

</td>

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">sys</span></span>

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="accc6e1bf582ffda3d446f39c6d88187711ded9a">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#accc6e1bf582ffda3d446f39c6d88187711ded9a"><strong>scripts/polya_training/dump_signal.py</strong></a>

<hr>

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

</td>

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

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python3</span></span>

</pre>

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

1

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<td class="diff-line-num 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">

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

</td>

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<td class="diff-line-num old_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">

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">dump_signal.py: take a **verbose** polya-call file and dump an HDF5 file with the signal data.</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

</pre>

</td>

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<br>

</li>

<li id="d20492b3a0e27e63052ed471166cee57a40c5cb9">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#d20492b3a0e27e63052ed471166cee57a40c5cb9"><strong>scripts/polya_training/hmmplot.py</strong></a>

<hr>

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</td>

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python3</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">Plot a random segmentation from a dataset.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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

</pre>

</td>

</tr>

</table>

<br>

</li>

<li id="a533feab8d3540e053620be917dd5fbf533458b2">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#a533feab8d3540e053620be917dd5fbf533458b2"><strong>scripts/polya_training/retrain_emission.py</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python3</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">retrain_emission.py: take an HDF5 file and segmentations, and output parameters of a mixture model.</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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<br>

</li>

<li id="30f30a527501f95bc409aa2919835ea54b6e1bba">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#30f30a527501f95bc409aa2919835ea54b6e1bba"><strong>scripts/reestimate_polya_emissions.py</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#! /usr/bin/env python3</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="s" style="color: #d14;">"""</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="s" style="color: #d14;">reestimate_polya_emissions.py: given two `polya-samples` TSV files based on different</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="python"><span class="s" style="color: #d14;">underlying kmer models (with the newer TSV giving failing poly(A) segmentations),</span></span>

</pre>

</td>

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<br>

</li>

<li id="58a43c64ead5187f569b28ec5ca98b313c48d7c7">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#58a43c64ead5187f569b28ec5ca98b313c48d7c7"><strong>src/common/nanopolish_common.h</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</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">@@ -18,7 +18,7 @@</td>

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "logsum.h"</span></span>

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

</pre>

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_NAME "nanopolish"</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "0.11.<span class="idiff left right">2</span>"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "0.11.<span class="idiff left right">3</span>"</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_BUGREPORT "https://github.com/jts/nanopolish/issues"</span></span>

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

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>

</pre>

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<br>

</li>

<li id="2d62e059707d17d6d88d86a4af4fce9c4c482e3d">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#2d62e059707d17d6d88d86a4af4fce9c4c482e3d"><strong>src/nanopolish_index.cpp</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="122" 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="122" 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">@@ -122,7 +122,7 @@ void index_path(ReadDB& read_db, const std::string& path, const std::multimap<st</td>

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<pre style="margin: 0;"> <span id="LC122" class="line" lang="cpp">                <span class="c1" style="color: #998; font-style: italic;">// recurse</span></span>

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<pre style="margin: 0;"> <span id="LC123" class="line" lang="cpp">                <span class="n" style="color: #333;">index_path</span><span class="p">(</span><span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="n" style="color: #333;">full_fn</span><span class="p">,</span> <span class="n" style="color: #333;">fast5_to_read_name_map</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="124" 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="LC124" class="line" lang="cpp">            <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_fast5</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old old_line" data-linenumber="125" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="125" 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="LC125" 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 class="idiff left">!</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_to_read_name_map</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">empty</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="126" 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="LC125" class="line" lang="cpp">                <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">in_map</span></span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp">                    <span class="n" style="color: #333;">index_file_from_map</span><span class="p">(</span><span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="n" style="color: #333;">full_fn</span><span class="p">,</span> <span class="n" style="color: #333;">fast5_to_read_name_map</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC127" class="line" lang="cpp">                <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

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<td class="diff-line-num old_line" data-linenumber="128" 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="LC128" class="line" lang="cpp">                    <span class="n" style="color: #333;">index_file_from_fast5</span><span class="p">(</span><span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="n" style="color: #333;">full_fn</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="176" 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="176" 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">@@ -176,7 +176,6 @@ void parse_sequencing_summary(const std::string& filename, std::multimap<std::st</td>

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<pre style="margin: 0;"> <span id="LC176" 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;">fields</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;">header</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>

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

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<pre style="margin: 0;"> <span id="LC178" 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;">string</span> <span class="n" style="color: #333;">READ_NAME_STR</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"read_id"</span><span class="p">;</span></span>

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<td class="diff-line-num old old_line" data-linenumber="179" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="179" 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="LC179" 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;">string</span> <span class="n" style="color: #333;">FILENAME_STR</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"filename"</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="180" 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="LC179" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">filename_idx</span> <span class="o" style="font-weight: 600;">=</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="LC180" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">read_name_idx</span> <span class="o" style="font-weight: 600;">=</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="LC181" class="line" lang="cpp"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="185" 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="184" 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">@@ -185,13 +184,14 @@ void parse_sequencing_summary(const std::string& filename, std::multimap<std::st</td>

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="cpp">            <span class="n" style="color: #333;">read_name_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="186" 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="LC185" class="line" lang="cpp">        <span class="p">}</span></span>

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<td class="diff-line-num old_line" data-linenumber="187" 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="LC186" class="line" lang="cpp"></span>

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<td class="diff-line-num old old_line" data-linenumber="188" 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="LC188" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">FILENAME_STR</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="189" 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="LC187" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// 19/11/05: support live basecalling summary files</span></span>

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<pre style="margin: 0;">+<span id="LC188" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"filename"</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">fields</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">==</span> <span class="s" style="color: #d14;">"filename_fast5"</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp">            <span class="n" style="color: #333;">filename_idx</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">i</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC192" class="line" lang="cpp"></span>

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<td class="diff-line-num old_line" data-linenumber="193" 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="LC193" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">filename_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new_line old" data-linenumber="194" 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="LC194" class="line" lang="cpp">        <span class="n" style="color: #333;">exit_bad_header</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">FILENAME_STR</span></span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

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<td class="diff-line-num new old_line" data-linenumber="195" 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="194" 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="LC194" class="line" lang="cpp">        <span class="n" style="color: #333;">exit_bad_header</span><span class="p">(</span><span class="s" style="color: #d14;"><span class="idiff left right">"fast5 filename"</span></span><span class="p">,</span> <span class="n" style="color: #333;">filename</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC196" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="197" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_name_idx</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</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">@@ -274,6 +274,32 @@ void parse_index_options(int argc, char** argv)</td>

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<pre style="margin: 0;"> <span id="LC274" class="line" lang="cpp">    <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reads_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">argv</span><span class="p">[</span><span class="n" style="color: #333;">optind</span><span class="o" style="font-weight: 600;">++</span><span class="p">];</span></span>

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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"><span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC277" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">clean_fast5_map</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;">multimap</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="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="o" style="font-weight: 600;">>&</span> <span class="n" style="color: #333;">mmap</span><span class="p">)</span></span>

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<pre style="margin: 0;">+<span id="LC278" class="line" lang="cpp"><span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC279" 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;">map</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="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">int</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">fast5_read_count</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC280" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">mmap</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC281" class="line" lang="cpp">        <span class="n" style="color: #333;">fast5_read_count</span><span class="p">[</span><span class="n" style="color: #333;">iter</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">]</span><span class="o" style="font-weight: 600;">++</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC282" class="line" lang="cpp">    <span class="p">}</span></span>

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<pre style="margin: 0;">+<span id="LC283" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC284" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">EXPECTED_ENTRIES_PER_FAST5</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4000</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC285" 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;">invalid_entries</span><span class="p">;</span></span>

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<td class="diff-line-num new new_line" data-linenumber="286" 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="LC286" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">iter</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fast5_read_count</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC287" class="line" lang="cpp">        <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">.</span><span class="n" style="color: #333;">second</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">EXPECTED_ENTRIES_PER_FAST5</span><span class="p">)</span> <span class="p">{</span></span>

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<td class="diff-line-num new new_line" data-linenumber="288" 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="LC288" class="line" lang="cpp">            <span class="c1" style="color: #998; font-style: italic;">//fprintf(stderr, "warning: %s has %d entries in the summary and will be indexed the slow way\n", iter.first.c_str(), iter.second);</span></span>

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<pre style="margin: 0;">+<span id="LC289" class="line" lang="cpp">            <span class="n" style="color: #333;">invalid_entries</span><span class="p">.</span><span class="n" style="color: #333;">push_back</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="p">.</span><span class="n" style="color: #333;">first</span><span class="p">);</span></span>

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<td class="diff-line-num new new_line" data-linenumber="290" 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">

290

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<pre style="margin: 0;">+<span id="LC290" class="line" lang="cpp">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="291" 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">

291

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

<pre style="margin: 0;">+<span id="LC291" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="292" 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">

292

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="293" 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">

293

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<pre style="margin: 0;">+<span id="LC293" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">invalid_entries</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">()</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">0</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="294" 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">

294

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<pre style="margin: 0;">+<span id="LC294" class="line" lang="cpp">        <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"warning: detected invalid summary file entries for %zu of %zu fast5 files</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">,</span> <span class="n" style="color: #333;">invalid_entries</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">(),</span> <span class="n" style="color: #333;">fast5_read_count</span><span class="p">.</span><span class="n" style="color: #333;">size</span><span class="p">());</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="295" 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">

295

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<pre style="margin: 0;">+<span id="LC295" class="line" lang="cpp">        <span class="n" style="color: #333;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"These files will be indexed without using the summary file, which is slow.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="296" 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">

296

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<pre style="margin: 0;">+<span id="LC296" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

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

<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="297" 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">

297

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

<pre style="margin: 0;">+<span id="LC297" class="line" lang="cpp"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="298" 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">

298

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<pre style="margin: 0;">+<span id="LC298" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">for</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="k" style="font-weight: 600;">auto</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fast5_name</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">invalid_entries</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="299" 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">

299

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

<pre style="margin: 0;">+<span id="LC299" class="line" lang="cpp">        <span class="n" style="color: #333;">mmap</span><span class="p">.</span><span class="n" style="color: #333;">erase</span><span class="p">(</span><span class="n" style="color: #333;">fast5_name</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="277" 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="300" 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">

300

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<pre style="margin: 0;">+<span id="LC300" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="301" 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">

301

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<pre style="margin: 0;">+<span id="LC301" class="line" lang="cpp"><span class="p">}</span></span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="277" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

<td class="diff-line-num new new_line" data-linenumber="302" 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">

302

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<pre style="margin: 0;">+<span id="LC302" class="line" lang="cpp"></span>

</pre>

</td>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="303" 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">

303

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<pre style="margin: 0;"> <span id="LC303" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="nf" style="color: #900; font-weight: 600;">index_main</span><span class="p">(</span><span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="kt" style="color: #458; font-weight: 600;">char</span><span class="o" style="font-weight: 600;">**</span> <span class="n" style="color: #333;">argv</span><span class="p">)</span></span>

</pre>

</td>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="304" 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">

304

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

<pre style="margin: 0;"> <span id="LC304" class="line" lang="cpp"><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="305" 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">

305

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<pre style="margin: 0;"> <span id="LC305" class="line" lang="cpp">    <span class="n" style="color: #333;">parse_index_options</span><span class="p">(</span><span class="n" style="color: #333;">argc</span><span class="p">,</span> <span class="n" style="color: #333;">argv</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="288" 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="314" 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">@@ -288,6 +314,13 @@ int index_main(int argc, char** argv)</td>

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<td class="diff-line-num old_line" data-linenumber="288" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="314" 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">

314

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<pre style="margin: 0;"> <span id="LC314" class="line" lang="cpp">        <span class="n" style="color: #333;">parse_sequencing_summary</span><span class="p">(</span><span class="n" style="color: #333;">ss_filename</span><span class="p">,</span> <span class="n" style="color: #333;">fast5_to_read_name_map</span><span class="p">);</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="289" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="315" 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">

315

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<pre style="margin: 0;"> <span id="LC315" class="line" lang="cpp">    <span class="p">}</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC316" class="line" lang="cpp"></span>

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<pre style="margin: 0;">+<span id="LC317" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Detect non-unique fast5 file names in the summary file</span></span>

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<pre style="margin: 0;">+<span id="LC318" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// This occurs when a file with the same name (abc_0.fast5) appears in both fast5_pass</span></span>

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<pre style="margin: 0;">+<span id="LC319" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// and fast5_fail. This will be fixed by ONT but in the meantime we check for</span></span>

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<pre style="margin: 0;">+<span id="LC320" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// fast5 files that have a non-standard number of reads (>4000) and remove them</span></span>

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<pre style="margin: 0;">+<span id="LC321" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// from the map. These fast5s will be indexed the slow way.</span></span>

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<pre style="margin: 0;">+<span id="LC322" class="line" lang="cpp">    <span class="n" style="color: #333;">clean_fast5_map</span><span class="p">(</span><span class="n" style="color: #333;">fast5_to_read_name_map</span><span class="p">);</span></span>

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<pre style="margin: 0;">+<span id="LC323" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC324" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// import read names, and possibly fast5 paths, from the fasta/fastq file</span></span>

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<pre style="margin: 0;"> <span id="LC325" class="line" lang="cpp">    <span class="n" style="color: #333;">ReadDB</span> <span class="n" style="color: #333;">read_db</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC326" class="line" lang="cpp">    <span class="n" style="color: #333;">read_db</span><span class="p">.</span><span class="n" style="color: #333;">build</span><span class="p">(</span><span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">reads_file</span><span class="p">);</span></span>

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<br>

</li>

<li id="ecc53e18e8deb4dabc0e2ec2afe10d1d4c114f91">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#ecc53e18e8deb4dabc0e2ec2afe10d1d4c114f91"><strong>src/nanopolish_phase_reads.cpp</strong></a>

<hr>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -59,7 +59,9 @@ SUBPROGRAM " Version " PACKAGE_VERSION "\n"</td>

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

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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="k" style="font-weight: 600;">static</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">char</span> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">PHASE_READS_USAGE_MESSAGE</span> <span class="o" style="font-weight: 600;">=</span></span>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"><span class="s" style="color: #d14;">"Usage: "</span> <span class="n" style="color: #333;">PACKAGE_NAME</span> <span class="s" style="color: #d14;">" "</span> <span class="n" style="color: #333;">SUBPROGRAM</span> <span class="s" style="color: #d14;">" [OPTIONS] --reads reads.fa --bam alignments.bam --genome genome.fa variants.vcf</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<td class="diff-line-num new_line old" data-linenumber="62" 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="LC62" class="line" lang="cpp"><span class="s" style="color: #d14;">"Train a duration model</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="cpp"><span class="s" style="color: #d14;">"Output a BAM file where each record shows the combination of alleles from variants.vcf that each read supports.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="cpp"><span class="s" style="color: #d14;">"variants.vcf can be any VCF file but only SNPs will be phased and variants that have a homozygous reference genotype (0/0)</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="cpp"><span class="s" style="color: #d14;">"will be skipped.</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="cpp"><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC66" class="line" lang="cpp"><span class="s" style="color: #d14;">"  -v, --verbose                        display verbose output</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>

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<pre style="margin: 0;"> <span id="LC67" class="line" lang="cpp"><span class="s" style="color: #d14;">"      --version                        display version</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</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">@@ -80,7 +82,7 @@ namespace opt</td>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</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;">genome_file</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</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;">variants_file</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC84" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</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;">region</span><span class="p">;</span></span>

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

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

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<pre style="margin: 0;"> <span id="LC86" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">progress</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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<pre style="margin: 0;"> <span id="LC87" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">num_threads</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="LC88" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">static</span> <span class="kt" style="color: #458; font-weight: 600;">unsigned</span> <span class="n" style="color: #333;">batch_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">128</span><span class="p">;</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="187" 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="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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -187,13 +189,13 @@ void phase_single_read(const ReadDB& read_db,</td>

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<pre style="margin: 0;"> <span id="LC189" class="line" lang="cpp">    <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">BAM_Q_OFFSET</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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<pre style="margin: 0;"> <span id="LC190" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">tid</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">omp_get_thread_num</span><span class="p">();</span></span>

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<pre style="margin: 0;"> <span id="LC191" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">alignment_flags</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">HAF_ALLOW_PRE_CLIP</span> <span class="o" style="font-weight: 600;">|</span> <span class="n" style="color: #333;">HAF_ALLOW_POST_CLIP</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="cpp"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC192" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC193" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// Load a squiggle read for the mapped read</span></span>

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<pre style="margin: 0;"> <span id="LC194" 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;">read_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_get_qname</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC195" class="line" lang="cpp"></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="196" 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="LC196" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// load read</span></span>

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<pre style="margin: 0;"> <span id="LC197" class="line" lang="cpp">    <span class="n" style="color: #333;">SquiggleRead</span> <span class="n" style="color: #333;">sr</span><span class="p">(</span><span class="n" style="color: #333;">read_name</span><span class="p">,</span> <span class="n" style="color: #333;">read_db</span><span class="p">);</span></span>

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<td class="diff-line-num new_line old" data-linenumber="198" 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="LC196" class="line" lang="cpp"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC198" class="line" lang="cpp"></span>

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<td class="diff-line-num new_line" data-linenumber="199" 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="LC199" 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;">ref_name</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">hdr</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">target_name</span><span class="p">[</span><span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">tid</span><span class="p">];</span></span>

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<td class="diff-line-num new_line" data-linenumber="200" 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="LC200" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignment_start_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">record</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">core</span><span class="p">.</span><span class="n" style="color: #333;">pos</span><span class="p">;</span></span>

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<td class="diff-line-num new_line" data-linenumber="201" 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="LC201" class="line" lang="cpp">    <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">alignment_end_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">bam_endpos</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">);</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="224" 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="226" 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">@@ -224,7 +226,7 @@ void phase_single_read(const ReadDB& read_db,</td>

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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp">                                                        <span class="n" style="color: #333;">alignment_start_pos</span><span class="p">,</span></span>

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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp">                                                        <span class="n" style="color: #333;">alignment_end_pos</span><span class="p">,</span></span>

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<td class="diff-line-num new_line" data-linenumber="228" 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="LC228" class="line" lang="cpp">                                                        <span class="o" style="font-weight: 600;">&</span><span class="n" style="color: #333;">fetched_len</span><span class="p">);</span></span>

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<td class="diff-line-num new_line old" data-linenumber="229" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC227" class="line" lang="cpp"><span class="idiff left right">    </span></span>

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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp">    <span class="c1" style="color: #998; font-style: italic;">// convert to upper case to avoid calling c>C as variants</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="231" 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="LC231" 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;">transform</span><span class="p">(</span><span class="n" style="color: #333;">reference_seq</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="n" style="color: #333;">reference_seq</span><span class="p">.</span><span class="n" style="color: #333;">end</span><span class="p">(),</span> <span class="n" style="color: #333;">reference_seq</span><span class="p">.</span><span class="n" style="color: #333;">begin</span><span class="p">(),</span> <span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">toupper</span><span class="p">);</span></span>

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<td class="diff-line-num new_line" data-linenumber="232" 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="LC232" class="line" lang="cpp"></span>

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<br>

</li>

<li id="8a4594db09bdbd5859ea2b82ef08bae7e6cb4eba">

<a href="https://salsa.debian.org/med-team/nanopolish/commit/4737abe338c38aeaa845de899aaf229d8a9bb0bd#8a4594db09bdbd5859ea2b82ef08bae7e6cb4eba"><strong>src/nanopolish_vcf2fasta.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">@@ -237,7 +237,7 @@ int vcf2fasta_main(int argc, char** argv)</td>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="cpp">        <span class="c1" style="color: #998; font-style: italic;">// make a vector holding either a literal character or an index to the variant that needs to be applied</span></span>

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<pre style="margin: 0;"> <span id="LC238" 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="kt" style="color: #458; font-weight: 600;">uint32_t</span><span class="o" style="font-weight: 600;">></span> <span class="n" style="color: #333;">consensus_record</span><span class="p">(</span><span class="n" style="color: #333;">length</span><span class="p">);</span></span>

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<pre style="margin: 0;"> <span id="LC239" 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;">size_t</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span><span class="p">;</span> <span class="n" style="color: #333;">i</span> <span class="o" style="font-weight: 600;"><</span> <span class="n" style="color: #333;">length</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="n" style="color: #333;">i</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">-<span id="LC240" class="line" lang="cpp">            <span class="n" style="color: #333;">consensus_record</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">seq</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">]</span>;</span></span>

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<pre style="margin: 0;">+<span id="LC240" class="line" lang="cpp">            <span class="n" style="color: #333;">consensus_record</span><span class="p">[</span><span class="n" style="color: #333;">i</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">toupper</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">seq</span></span><span class="p"><span class="idiff">[</span></span><span class="n" style="color: #333;"><span class="idiff">i</span></span><span class="p"><span class="idiff right">])</span>;</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="cpp">        <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="cpp"></span>

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<pre style="margin: 0;"> <span id="LC243" class="line" lang="cpp">        <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">num_skipped</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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