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<h3>
Andreas Tille 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/7868af613b689fbb895f987c5608a25cb8c32549">7868af61</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-07-10T11:12:03Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.11.1</pre>
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<h4>10 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#a5cc2925ca8258af241be7e5b0381edf30266302">
.gitignore
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<li class="file-stats">
<a href="#dea01dd89a3b602828e630677fde5d77c06441c8">
.travis.yml
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<li class="file-stats">
<a href="#c42ce8cf10fee4d8f4d8f559f15f4f390d23513e">
<span class="new-file">
+
Dockerfile-arm
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<li class="file-stats">
<a href="#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c">
Makefile
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<li class="file-stats">
<a href="#62df078594b947ca6f787a59ae6ddefabce9fcad">
docs/source/index.rst
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<li class="file-stats">
<a href="#2d2c9c258608b174cf4fe4c3a5ad976a13fc99ca">
docs/source/manual.rst
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<li class="file-stats">
<a href="#41660adec78594f229c01b0235788ce15e4799e4">
scripts/calculate_methylation_frequency.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>
<li class="file-stats">
<a href="#3e7589d9f810f7643a9b0d6c2e885784173011a1">
src/nanopolish_polya_estimator.cpp
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</ul>
<h4>Changes:</h4>
<li id="a5cc2925ca8258af241be7e5b0381edf30266302">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#a5cc2925ca8258af241be7e5b0381edf30266302"><strong>.gitignore</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -17,7 +17,7 @@ include/</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">lib/</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">share/</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext">hdf5-1.<span class="idiff left right">8.14</span>.tar.gz</span>
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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">
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">hdf5-1.<span class="idiff left right">*</span>.tar.gz</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">3.2.5.tar.bz2</span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext">eigen/</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext">local*</span></pre>
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<li id="dea01dd89a3b602828e630677fde5d77c06441c8">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#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>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="yaml"></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="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="yaml"><span class="na" style="color: #008080;">dist</span><span class="pi">:</span> <span class="s" style="color: #d14;">trusty</span></span>
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<td class="diff-line-num new old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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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>
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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">
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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;">sudo</span><span class="pi">:</span> <span class="no" style="color: #008080;">false</span></span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(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="LC6" 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>
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<td class="diff-line-num old_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
6
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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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>
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<td class="diff-line-num old_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
7
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="yaml"><span class="na" style="color: #008080;">git</span><span class="pi">:</span></span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="yaml"> <span class="na" style="color: #008080;">depth</span><span class="pi">:</span> <span class="s" style="color: #d14;">1</span></span>
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<td class="diff-line-num new_line" data-linenumber="10" style="width: 35px; color: rgba(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="LC10" class="line" lang="yaml"></span>
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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">
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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>
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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">
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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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13
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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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14
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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>
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15
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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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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="yaml"> <span class="no" style="color: #008080;">sed -i "/^FROM / s/arm64/${ARCH}/" Dockerfile-arm</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="yaml"> <span class="no" style="color: #008080;">docker run --rm --privileged \</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="yaml"> <span class="no" style="color: #008080;">multiarch/qemu-user-static:register --reset && \</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="yaml"> <span class="no" style="color: #008080;">docker build --rm -t nanopolish -f Dockerfile-arm .</span></span>
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22
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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>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="pi">|</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="yaml"> <span class="no" style="color: #008080;">docker run --rm -t \</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="yaml"> <span class="no" style="color: #008080;">-e HDF5="${HDF5:-install}" \</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="yaml"> <span class="no" style="color: #008080;">-e H5_CFLAGS="${H5_CFLAGS}" \</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="yaml"> <span class="no" style="color: #008080;">-e H5_INCLUDE="${H5_INCLUDE}" \</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="yaml"> <span class="no" style="color: #008080;">-e LDFLAGS="${LDFLAGS}" \</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="yaml"> <span class="no" style="color: #008080;">nanopolish</span></span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="yaml"></span>
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10
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31
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="yaml"><span class="na" style="color: #008080;">matrix</span><span class="pi">:</span></span>
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11
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="yaml"> <span class="na" style="color: #008080;">include</span><span class="pi">:</span></span>
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12
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Set env for both nanoplish and the dependency hdf5.</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CC=gcc-4.8</span></span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CXX=g++-4.8</span></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">AR=gcc-ar-4.8</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">NM=gcc-nm-4.8</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">RANLIB=gcc-ranlib-4.8</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CC=gcc-8</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CXX=g++-8</span></span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">AR=gcc-ar-8</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">NM=gcc-nm-8</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">RANLIB=gcc-ranlib-8</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Set env for both nanoplish and the dependency hdf5.</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CC=gcc-4.8</span></span>
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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;">CXX=g++-4.8</span></span>
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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;">AR=gcc-ar-4.8</span></span>
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38
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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;">NM=gcc-nm-4.8</span></span>
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39
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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;">RANLIB=gcc-ranlib-4.8</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="yaml"> <span class="pi">-</span> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">CC=gcc-8</span></span>
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42
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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;">CXX=g++-8</span></span>
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43
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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;">AR=gcc-ar-8</span></span>
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44
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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;">NM=gcc-nm-8</span></span>
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45
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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;">RANLIB=gcc-ranlib-8</span></span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># aarch64 - ARM 64-bit</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" 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>
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48
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<pre style="margin: 0;">+<span id="LC48" 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>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ARCH=arm64</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*arch</span></span>
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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;">*cron-only</span></span>
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<pre style="margin: 0;">+<span id="LC53" 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>
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<pre style="margin: 0;">+<span id="LC54" 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>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ARCH=arm64</span></span>
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57
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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;">HDF5="system"</span></span>
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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;">H5_INCLUDE="-I/usr/include/hdf5/serial"</span></span>
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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;">LDFLAGS="-L/usr/lib/aarch64-linux-gnu/hdf5/serial"</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*arch</span></span>
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<pre style="margin: 0;">+<span id="LC61" 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="LC62" 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>
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63
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<pre style="margin: 0;">+<span id="LC63" 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>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ARCH=armhf</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*arch</span></span>
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67
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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;">*cron-only</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" 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>
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<pre style="margin: 0;">+<span id="LC69" 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>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="yaml"> <span class="na" style="color: #008080;">env</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">ARCH=armhf</span></span>
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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;">HDF5="system"</span></span>
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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;">H5_INCLUDE="-I/usr/include/hdf5/serial"</span></span>
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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;">LDFLAGS="-L/usr/lib/arm-linux-gnueabihf/hdf5/serial"</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="yaml"> <span class="s" style="color: #d14;"><<</span><span class="pi">:</span> <span class="nv" style="color: #008080;">*arch</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="yaml"> <span class="na" style="color: #008080;">allow_failures</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC77" 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>
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<pre style="margin: 0;">+<span id="LC78" 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>
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<pre style="margin: 0;">+<span id="LC79" 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>
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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;">armv7l</span></span>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="yaml"></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="yaml"><span class="c1" style="color: #998; font-style: italic;"># Install and export newer gcc</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="yaml"><span class="na" style="color: #008080;">before_install</span><span class="pi">:</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">@@ -38,9 +94,11 @@ before_install:</td>
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="yaml"> <span class="no" style="color: #008080;">sudo apt-get install -qq "${CXX}"</span></span>
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="yaml"> <span class="no" style="color: #008080;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="yaml"></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="yaml"><span class="na" style="color: #008080;"><span class="idiff left right">before_</span>script</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Suppress all compiler warnings for hdf5 Makefile</span></span>
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># to display the log without downloading the raw log on Travis log page.</span></span>
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<pre style="margin: 0;"> <span id="LC100" class="line" lang="yaml"> <span class="c1" style="color: #998; font-style: italic;"># Travis finishs with error when exceeding the limit of 4 MB of log length.</span></span>
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">export H5_CFLAGS="-w"</span></span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="yaml"></span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="yaml"><span class="na" style="color: #008080;">script</span><span class="pi">:</span></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="yaml"> <span class="pi">-</span> <span class="s" style="color: #d14;">make && make test</span></span></pre>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#c42ce8cf10fee4d8f4d8f559f15f4f390d23513e"><strong>Dockerfile-arm</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">FROM multiarch/ubuntu-debootstrap:arm64-bionic</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">RUN uname -a</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">RUN apt-get update -qq && \</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> apt-get install -yq --no-install-suggests --no-install-recommends \</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> bzip2 \</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> ca-certificates \</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> gcc \</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> g++ \</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> make \</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> software-properties-common</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">RUN add-apt-repository -y universe && \</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> apt-get update -qq && \</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> apt-get install -yq libhdf5-dev</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">RUN find /usr/include -name "hdf5.h" || true</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">RUN find /usr/lib -name "libhdf5.a" || true</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">WORKDIR /nanopolish</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">COPY . .</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">CMD exec bash -c "make && make test"</span></pre>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#836efb6e25a091dcb4ff8e1dbb2f0be6a5cbf14c"><strong>Makefile</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">@@ -12,6 +12,7 @@ LIBS = -lz</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: #000080;">-g</span> <span class="nt" style="color: #000080;">-O3</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="make"><span class="nv" style="color: #008080;">CXXFLAGS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c++11 <span class="nt" style="color: #000080;">-fopenmp</span> <span class="nt" style="color: #000080;">-fsigned-char</span> <span class="nt" style="color: #000080;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 <span class="c" style="color: #998; font-style: italic;">#D_FILE_OFFSET_BITS=64 makes nanopolish work in 32 bit systems</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="make"><span class="nv" style="color: #008080;">CFLAGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: #000080;">-O3</span> <span class="nt" style="color: #000080;">-std</span><span class="o" style="font-weight: 600;">=</span>c99 <span class="nt" style="color: #000080;">-fsigned-char</span> <span class="nt" style="color: #000080;">-D_FILE_OFFSET_BITS</span><span class="o" style="font-weight: 600;">=</span>64 </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="make"><span class="nv" style="color: #008080;">LDFLAGS</span> <span class="o" style="font-weight: 600;">?=</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="make"><span class="nv" style="color: #008080;">CXX</span> <span class="o" style="font-weight: 600;">?=</span> g++</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="make"><span class="nv" style="color: #008080;">CC</span> <span class="o" style="font-weight: 600;">?=</span> gcc</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="make"></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">@@ -20,8 +21,7 @@ HDF5 ?= install</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make"><span class="nv" style="color: #008080;">EIGEN</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="make"><span class="nv" style="color: #008080;">HTS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nb" style="color: #0086b3;">install</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="make"></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="make"><span class="nv" style="color: #008080;">HDF5_VERSION</span> <span class="o" style="font-weight: 600;">?=</span> 1.8.14</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="make"><span class="nv" style="color: #008080;">HDF5_CONFIG_ARGS</span> <span class="o" style="font-weight: 600;">?=</span> <span class="nt" style="color: #000080;">--enable-threadsafe</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="make"><span class="nv" style="color: #008080;">HDF5_VERSION</span> <span class="o" style="font-weight: 600;">?=</span> 1.10.4</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="make"><span class="nv" style="color: #008080;">EIGEN_VERSION</span> <span class="o" style="font-weight: 600;">?=</span> 3.2.5</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="make"></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Check operating system, OSX doesn't have -lrt</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">@@ -38,7 +38,7 @@ ifeq ($(HDF5), install)</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">else</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="make"> <span class="c" style="color: #998; font-style: italic;"># Use system-wide hdf5</span></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="make"> <span class="nv" style="color: #008080;">H5_LIB</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">-<span id="LC41" class="line" lang="make"> <span class="nv" style="color: #008080;">H5_INCLUDE</span> <span class="o" style="font-weight: 600;">=</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="make"> <span class="nv" style="color: #008080;">H5_INCLUDE</span> <span class="o" style="font-weight: 600;"><span class="idiff left right">?</span>=</span></span>
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<pre style="margin: 0;"> <span id="LC42" class="line" lang="make"> <span class="nv" style="color: #008080;">LIBS</span> <span class="o" style="font-weight: 600;">+=</span> <span class="nt" style="color: #000080;">-lhdf5</span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">endif</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="make"></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">@@ -91,13 +91,13 @@ htslib/libhts.a:</td>
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<pre style="margin: 0;"> <span id="LC91" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;">#</span></span>
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<pre style="margin: 0;"> <span id="LC92" class="line" lang="make"><span class="nl">lib/libhdf5.a</span><span class="o" style="font-weight: 600;">:</span></span>
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="make"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: #000080;">-e</span> hdf5-<span class="nv" style="color: #008080;">$(HDF5_VERSION)</span>.tar.gz <span class="o" style="font-weight: 600;">]</span><span class="p">;</span> <span class="k" style="font-weight: 600;">then</span> <span class="se" style="color: #d14;">\</span></span>
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94
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="make"> <span class="nv" style="color: #008080;">version_major_min<span class="idiff left right">i</span>or</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(HDF5_VERSION)</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-E</span> <span class="s1" style="color: #d14;">'s/\.[0-9]+$$//'</span><span class="sb" style="color: #d14;">`</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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95
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="make"> wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-<span class="nv" style="color: #008080;">$$</span><span class="o" style="font-weight: 600;">{</span>version_major_min<span class="idiff left right">i</span>or<span class="o" style="font-weight: 600;">}</span>/hdf5-<span class="nv" style="color: #008080;">$(HDF5_VERSION)</span>/src/hdf5-<span class="nv" style="color: #008080;">$(HDF5_VERSION)</span>.tar.gz<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="make"> <span class="nv" style="color: #008080;">version_major_minor</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">echo</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$(HDF5_VERSION)</span><span class="s2" style="color: #d14;">"</span> | <span class="nb" style="color: #0086b3;">sed</span> <span class="nt" style="color: #000080;">-E</span> <span class="s1" style="color: #d14;">'s/\.[0-9]+$$//'</span><span class="sb" style="color: #d14;">`</span><span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="make"> wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-<span class="nv" style="color: #008080;">$$</span><span class="o" style="font-weight: 600;">{</span>version_major_minor<span class="o" style="font-weight: 600;">}</span>/hdf5-<span class="nv" style="color: #008080;">$(HDF5_VERSION)</span>/src/hdf5-<span class="nv" style="color: #008080;">$(HDF5_VERSION)</span>.tar.gz<span class="p">;</span> <span class="se" style="color: #d14;">\</span></span>
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96
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="make"> <span class="k" style="font-weight: 600;">fi</span></span>
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<td class="diff-line-num old_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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<td class="diff-line-num new_line" data-linenumber="97" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="make"></span>
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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">
98
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<td class="diff-line-num new_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">
98
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">tar</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">-xzf</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">hdf5-$(HDF5_VERSION).tar.gz</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">||</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">exit</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">255</span></span>
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99
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<td class="diff-line-num new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
99
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<pre style="margin: 0;"> <span id="LC99" class="line" lang="make"> <span class="err" style="color: #a61717; background-color: #e3d2d2;">cd</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">hdf5-$(HDF5_VERSION)</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">&&</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span></span>
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100
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="make"><span class="idiff left"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">./configure</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">--enable-threadsafe</span></span> <span class="nv" style="color: #008080;">--libdir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/../lib <span class="nt" style="color: #000080;">--includedir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/../include <span class="nt" style="color: #000080;">--prefix</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/.. <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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<td class="diff-line-num new old_line" data-linenumber="101" 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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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="make"><span class="idiff left"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">./configure</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff">--enable-threadsafe</span></span><span class="idiff"> </span><span class="err" style="color: #a61717; background-color: #e3d2d2;"><span class="idiff right">--disable-hl</span></span> <span class="nv" style="color: #008080;">--libdir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/../lib <span class="nt" style="color: #000080;">--includedir</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/../include <span class="nt" style="color: #000080;">--prefix</span><span class="o" style="font-weight: 600;">=</span><span class="sb" style="color: #d14;">`</span><span class="nb" style="color: #0086b3;">pwd</span><span class="sb" style="color: #d14;">`</span>/.. <span class="o" style="font-weight: 600;">&&</span> <span class="se" style="color: #d14;">\</span></span>
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101
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101
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<pre style="margin: 0;"> <span id="LC101" class="line" lang="make"> make <span class="o" style="font-weight: 600;">&&</span> make <span class="nb" style="color: #0086b3;">install</span></span>
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102
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102
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="make"></span>
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<td class="diff-line-num old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
103
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103
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="make"><span class="c" style="color: #998; font-style: italic;"># Download and install eigen if not already downloaded</span></span>
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<li id="62df078594b947ca6f787a59ae6ddefabce9fcad">
<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#62df078594b947ca6f787a59ae6ddefabce9fcad"><strong>docs/source/index.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">@@ -15,6 +15,7 @@ nanopolish</td>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> quickstart_consensus</span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> quickstart_eventalign</span>
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17
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17
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> quickstart_call_methylation</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> quickstart_polya</span>
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18
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<td class="diff-line-num new_line" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> debug</span>
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19
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> manual</span>
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20
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21
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#2d2c9c258608b174cf4fe4c3a5ad976a13fc99ca"><strong>docs/source/manual.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">@@ -11,6 +11,7 @@ Modules available: ::</td>
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> nanopolish variants --consensus: calculate an improved consensus sequence for a draft genome assembly</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> nanopolish eventalign: align signal-level events to k-mers of a reference genome</span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> nanopolish phase-reads: Phase reads using heterozygous SNVs with respect to a reference genome </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> nanopolish polya: Estimate polyadenylated tail lengths on native RNA reads</span>
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14
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">|</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">extract</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">@@ -486,3 +487,63 @@ Usage example</td>
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487
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<pre style="margin: 0;"> <span id="LC487" class="line" lang="plaintext"> - print out a progress message</span>
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<pre style="margin: 0;"> <span id="LC488" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC489" class="line" lang="plaintext"> </span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="plaintext">polya</span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="plaintext">--------------------</span>
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492
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="plaintext">Overview</span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="plaintext">"""""""""""""""""""""""</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="plaintext"></span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="plaintext">Estimate the number of nucleotides in the poly(A) tails of native RNA reads.</span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="plaintext"></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="plaintext">Input</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="plaintext">"""""""""""""""""""""""</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="plaintext"> * basecalled reads</span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="plaintext"> * alignment information</span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="plaintext"> * reference transcripts</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="plaintext"></span>
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505
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="plaintext">Usage example</span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="plaintext">"""""""""""""""""""""""</span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="plaintext"></span>
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508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="plaintext">::</span>
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509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="plaintext"></span>
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510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="plaintext"> nanopolish polya [OPTIONS] --reads=reads.fa --bam=alignments.bam --genome=ref.fa</span>
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511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="plaintext"></span>
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512
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<pre style="margin: 0;">+<span id="LC512" class="line" lang="plaintext">.. list-table::</span>
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513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="plaintext"> :widths: 20 10 20 50</span>
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514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="plaintext"> :header-rows: 1</span>
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515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="plaintext"></span>
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516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="plaintext"> * - Argument name(s)</span>
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517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="plaintext"> - Required</span>
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518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="plaintext"> - Default value</span>
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519
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<pre style="margin: 0;">+<span id="LC519" class="line" lang="plaintext"> - Description</span>
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520
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<pre style="margin: 0;">+<span id="LC520" class="line" lang="plaintext"></span>
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521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="plaintext"> * - ``-w, --window=STR``</span>
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522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="plaintext"> - N</span>
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523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="plaintext"> - NA</span>
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524
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<pre style="margin: 0;">+<span id="LC524" class="line" lang="plaintext"> - Compute only for reads aligning to window of reference STR (format : ctg:start_id-end_id)</span>
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525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="plaintext"></span>
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526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="plaintext"> * - ``-r, --reads=FILE``</span>
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527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="plaintext"> - Y</span>
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528
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<pre style="margin: 0;">+<span id="LC528" class="line" lang="plaintext"> - NA</span>
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529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="plaintext"> - the FAST(A/Q) file of native RNA reads</span>
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530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="plaintext"></span>
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531
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<pre style="margin: 0;">+<span id="LC531" class="line" lang="plaintext"> * - ``-b, --bam=FILE``</span>
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532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="plaintext"> - Y</span>
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533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="plaintext"> - NA</span>
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534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="plaintext"> - the BAM file of alignments between reads and the reference</span>
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535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="plaintext"></span>
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536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="plaintext"> * - ``-g, --genome=FILE``</span>
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537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="plaintext"> - Y</span>
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538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="plaintext"> - NA</span>
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539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="plaintext"> - the reference transcripts</span>
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540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="plaintext"></span>
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541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="plaintext"> * - ``-t, --threads=NUM``</span>
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542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="plaintext"> - N</span>
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543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="plaintext"> - 1</span>
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544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="plaintext"> - use NUM threads</span>
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545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="plaintext"></span>
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546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="plaintext"> * - ``-v, -vv``</span>
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547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="plaintext"> - N</span>
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548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="plaintext"> - NA</span>
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="plaintext"> - `-v` returns raw sample log-likelihoods, while `-vv` returns event durations</span></pre>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#41660adec78594f229c01b0235788ce15e4799e4"><strong>scripts/calculate_methylation_frequency.py</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,17 +6,9 @@ import csv</td>
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">argparse</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;">collections</span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">namedtuple</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">make_key</span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">s</span><span class="p">)</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">":"</span> <span class="o" style="font-weight: 600;">+</span> <span class="nb" style="color: #0086b3;">str</span><span class="p">(</span><span class="n" style="color: #333;">e</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="python"><span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">split_key</span><span class="p">(</span><span class="n" style="color: #333;">k</span><span class="p">):</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">k</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split</span><span class="p">(</span><span class="s" style="color: #d14;">":"</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="python"> <span class="k" style="font-weight: 600;">return</span> <span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">],</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]),</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">f</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]))</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="python"><span class="k" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">SiteStats</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="python"> <span class="k" style="font-weight: 600;">def</span> <span class="nf" style="color: #900; font-weight: 600;">__init__</span><span class="p">(</span><span class="bp" style="color: #999;">self</span><span class="p">,</span> <span class="n" style="color: #333;">g_size</span><span class="p">,</span> <span class="n" style="color: #333;">g_seq</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">num_reads</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">posterior_methylated</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">called_sites</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">called_sites_methylated</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">0</span></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="python"> <span class="bp" style="color: #999;">self</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group_size</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">g_size</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">@@ -60,7 +52,7 @@ for record in csv_reader:</td>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="python"> </span>
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<pre style="margin: 0;"> <span id="LC53" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># if this is a multi-cpg group and split_groups is set, break up these sites</span></span>
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<pre style="margin: 0;"> <span id="LC54" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">args</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">split_groups</span> <span class="ow" style="font-weight: 600;">and</span> <span class="n" style="color: #333;">num_sites</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="LC63" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">record</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff right">]</span></span> </span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="python"> <span class="n" style="color: #333;">c</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff right">])</span></span> </span>
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="python"> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'start'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="python"> <span class="n" style="color: #333;">e</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">int</span><span class="p">(</span><span class="n" style="color: #333;">record</span><span class="p">[</span><span class="s" style="color: #d14;">'end'</span><span class="p">])</span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="python"></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">@@ -69,20 +61,20 @@ for record in csv_reader:</td>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="python"> <span class="n" style="color: #333;">cg_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="python"> <span class="n" style="color: #333;">first_cg_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">cg_pos</span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="python"> <span class="k" style="font-weight: 600;">while</span> <span class="n" style="color: #333;">cg_pos</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="LC72" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left right">make_key</span></span><span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cg_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">first_cg_pos</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cg_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">first_cg_pos</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cg_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">first_cg_pos</span><span class="p">,</span> <span class="n" style="color: #333;">s</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">cg_pos</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">first_cg_pos</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="python"> <span class="n" style="color: #333;">update_call_stats</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="mi" style="color: #099;">1</span><span class="p">,</span> <span class="n" style="color: #333;">is_methylated</span><span class="p">,</span> <span class="s" style="color: #d14;">"split-group"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="python"> <span class="n" style="color: #333;">cg_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">sequence</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">find</span><span class="p">(</span><span class="s" style="color: #d14;">"CG"</span><span class="p">,</span> <span class="n" style="color: #333;">cg_pos</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="LC67" class="line" lang="python"> <span class="k" style="font-weight: 600;">else</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;"><span class="idiff left">make_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">],</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'end'</span></span><span class="p"><span class="idiff right">]</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="python"> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="p"><span class="idiff left">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">str</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'chromosome'</span></span><span class="p"><span class="idiff">]),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'start'</span></span><span class="p"><span class="idiff">]),</span></span><span class="idiff"> </span><span class="nb" style="color: #0086b3;"><span class="idiff">int</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">record</span></span><span class="p"><span class="idiff">[</span></span><span class="s" style="color: #d14;"><span class="idiff">'end'</span></span><span class="p"><span class="idiff right">])</span>)</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="python"> <span class="n" style="color: #333;">update_call_stats</span><span class="p">(</span><span class="n" style="color: #333;">key</span><span class="p">,</span> <span class="n" style="color: #333;">num_sites</span><span class="p">,</span> <span class="n" style="color: #333;">is_methylated</span><span class="p">,</span> <span class="n" style="color: #333;">sequence</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># header</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="python"><span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="se" style="color: #d14;">\t</span><span class="s" style="color: #d14;">"</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">([</span><span class="s" style="color: #d14;">"chromosome"</span><span class="p">,</span> <span class="s" style="color: #d14;">"start"</span><span class="p">,</span> <span class="s" style="color: #d14;">"end"</span><span class="p">,</span> <span class="s" style="color: #d14;">"num_motifs_in_group"</span><span class="p">,</span> <span class="s" style="color: #d14;">"called_sites"</span><span class="p">,</span> <span class="s" style="color: #d14;">"called_sites_methylated"</span><span class="p">,</span> <span class="s" style="color: #d14;">"methylated_frequency"</span><span class="p">,</span> <span class="s" style="color: #d14;">"group_sequence"</span><span class="p">]))</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="python"></span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="python"><span class="n" style="color: #333;">sorted_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">(),</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left">split_key</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">x</span></span><span class="p"><span class="idiff right">)</span>)</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="python"><span class="n" style="color: #333;">sorted_keys</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">sorted</span><span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">(),</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">lambda</span> <span class="n" style="color: #333;">x</span><span class="p">:</span> <span class="n" style="color: #333;"><span class="idiff left right">x</span></span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">key</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">sorted_keys</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">called_sites</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="LC86" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span><span class="o" style="font-weight: 600;"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">split</span></span><span class="p"><span class="idiff">(</span></span><span class="s" style="color: #d14;"><span class="idiff">":"</span></span><span class="p"><span class="idiff right">)</span></span></span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="python"> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">)</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">key</span></span>
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87
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"> <span class="n" style="color: #333;">f</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">float</span><span class="p">(</span><span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">called_sites_methylated</span><span class="p">)</span> <span class="o" style="font-weight: 600;">/</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">called_sites</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span><span class="p">(</span><span class="s" style="color: #d14;">"</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">d</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%.3</span><span class="s" style="color: #d14;">f</span><span class="se" style="color: #d14;">\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> <span class="o" style="font-weight: 600;">%</span> <span class="p">(</span><span class="n" style="color: #333;">c</span><span class="p">,</span> <span class="n" style="color: #333;">s</span><span class="p">,</span> <span class="n" style="color: #333;">e</span><span class="p">,</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">group_size</span><span class="p">,</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">called_sites</span><span class="p">,</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">called_sites_methylated</span><span class="p">,</span> <span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="n" style="color: #333;">sites</span><span class="p">[</span><span class="n" style="color: #333;">key</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sequence</span><span class="p">))</span></span></pre>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#58a43c64ead5187f569b28ec5ca98b313c48d7c7"><strong>src/common/nanopolish_common.h</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -18,7 +18,7 @@</td>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="c"><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="c"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_NAME "nanopolish"</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "0.11.<span class="idiff left right">0</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="c"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "0.11.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="c"><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="c"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="c"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#2d62e059707d17d6d88d86a4af4fce9c4c482e3d"><strong>src/nanopolish_index.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">@@ -56,7 +56,7 @@ namespace opt</td>
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<pre style="margin: 0;"> <span id="LC56" 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;">ostream</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">os_p</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">index_file_from_map</span><span class="p">(</span><span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">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="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;">fast5_to_read_name_map</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">index_file_from_map</span><span class="p">(</span><span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fn</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">m<span class="idiff left right">ultim</span>ap</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;">fast5_to_read_name_map</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC60" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="cpp"> <span class="n" style="color: #333;">PROFILE_FUNC</span><span class="p">(</span><span class="s" style="color: #d14;">"index_file_from_map"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="cpp"></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -64,20 +64,16 @@ void index_file_from_map(ReadDB& read_db, const std::string& fn, const std::map<</td>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">size_t</span> <span class="n" style="color: #333;">last_dir_pos</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fn</span><span class="p">.</span><span class="n" style="color: #333;">find_last_of</span><span class="p">(</span><span class="s" style="color: #d14;">"/"</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC65" 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;">fast5_basename</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">last_dir_pos</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;">npos</span> <span class="o" style="font-weight: 600;">?</span> <span class="n" style="color: #333;">fn</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">fn</span><span class="p">.</span><span class="n" style="color: #333;">substr</span><span class="p">(</span><span class="n" style="color: #333;">last_dir_pos</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="LC66" class="line" lang="cpp"></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">const</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">auto</span></span><span class="o" style="font-weight: 600;"><span class="idiff">&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">iter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fast5_to_read_name_map</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">find</span></span><span class="p">(</span><span class="n" style="color: #333;">fast5_basename</span><span class="p">);</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">if</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">iter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fast5_to_read_name_map</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">end</span></span><span class="p"><span class="idiff right">()</span>)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">auto</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">range</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">fast5_to_read_name_map</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff right">equal_range</span></span><span class="p">(</span><span class="n" style="color: #333;">fast5_basename</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="cpp"> <span class="k" style="font-weight: 600;"><span class="idiff left">for</span></span><span class="p"><span class="idiff">(</span></span><span class="k" style="font-weight: 600;"><span class="idiff">auto</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">iter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">range</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">first</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">iter</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">!=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">range</span></span><span class="p"><span class="idiff">.</span></span><span class="n" style="color: #333;"><span class="idiff">second</span></span><span class="p"><span class="idiff">;</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">++</span></span><span class="n" style="color: #333;"><span class="idiff right">iter</span></span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="n" style="color: #333;">read_db</span><span class="p">.</span><span class="n" style="color: #333;">has_read</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">))</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="cpp"> <span class="n" style="color: #333;">read_db</span><span class="p">.</span><span class="n" style="color: #333;">add_signal_path</span><span class="p">(</span><span class="n" style="color: #333;">iter</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">second</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">(),</span> <span class="n" style="color: #333;">fn</span><span class="p">);</span></span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">-<span id="LC72" 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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<pre style="margin: 0;">-<span id="LC73" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">verbose</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>
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<pre style="margin: 0;">-<span id="LC74" 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;">"Could not find read %s in sequencing summary file</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;">fn</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC72" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">index_file_from_fast5</span><span class="p">(</span><span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fn</span><span class="p"><span class="idiff left">,</span></span><span class="idiff"> </span><span class="k" style="font-weight: 600;"><span class="idiff">const</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">map</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">string</span></span><span class="o" style="font-weight: 600;"><span class="idiff">>&</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fast5_to_read_name_map</span></span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">index_file_from_fast5</span><span class="p">(</span><span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">fn</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="cpp"> <span class="n" style="color: #333;">PROFILE_FUNC</span><span class="p">(</span><span class="s" style="color: #d14;">"index_file_from_fast5"</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="106" style="width: 35px; color: rgba(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">@@ -106,7 +102,7 @@ void index_file_from_fast5(ReadDB& read_db, const std::string& fn, const std::ma</td>
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<pre style="margin: 0;"> <span id="LC102" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC103" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC104" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<pre style="margin: 0;">-<span id="LC109" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">index_path</span><span class="p">(</span><span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">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="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;">fast5_to_read_name_map</span><span class="p">)</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">index_path</span><span class="p">(</span><span class="n" style="color: #333;">ReadDB</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">read_db</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">path</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">m<span class="idiff left right">ultim</span>ap</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;">fast5_to_read_name_map</span><span class="p">)</span></span>
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110
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106
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<pre style="margin: 0;"> <span id="LC106" class="line" lang="cpp"><span class="p">{</span></span>
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111
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<td class="diff-line-num new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
107
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<pre style="margin: 0;"> <span id="LC107" 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;">"[readdb] indexing %s</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;">path</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num old_line" data-linenumber="112" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
112
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<td class="diff-line-num new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
108
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<pre style="margin: 0;"> <span id="LC108" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">is_directory</span><span class="p">(</span><span class="n" style="color: #333;">path</span><span class="p">))</span> <span class="p">{</span></span>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="120" style="width: 35px; color: rgba(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">@@ -124,7 +120,7 @@ void index_path(ReadDB& read_db, const std::string& path, const std::map<std::st</td>
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124
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120
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<pre style="margin: 0;"> <span id="LC120" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span><span class="p">(</span><span class="o" style="font-weight: 600;">!</span><span class="n" style="color: #333;">fast5_to_read_name_map</span><span class="p">.</span><span class="n" style="color: #333;">empty</span><span class="p">())</span> <span class="p">{</span></span>
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125
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121
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<pre style="margin: 0;"> <span id="LC121" 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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<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">
126
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122
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<pre style="margin: 0;"> <span id="LC122" 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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127
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<pre style="margin: 0;">-<span id="LC127" 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 class="idiff left">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">fast5_to_read_name_map</span></span><span class="p">);</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" 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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128
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124
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<pre style="margin: 0;"> <span id="LC124" class="line" lang="cpp"> <span class="p">}</span></span>
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129
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125
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<pre style="margin: 0;"> <span id="LC125" class="line" lang="cpp"> <span class="p">}</span></span>
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130
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126
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<pre style="margin: 0;"> <span id="LC126" class="line" lang="cpp"> <span class="p">}</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="160" style="width: 35px; color: rgba(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="156" style="width: 35px; color: rgba(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">@@ -160,7 +156,7 @@ void exit_bad_header(const std::string& str, const std::string& filename)</td>
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<pre style="margin: 0;"> <span id="LC156" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC157" class="line" lang="cpp"></span>
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162
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158
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<pre style="margin: 0;"> <span id="LC158" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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163
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<pre style="margin: 0;">-<span id="LC163" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">parse_sequencing_summary</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</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;">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="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;">out_map</span><span class="p">)</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="cpp"><span class="kt" style="color: #458; font-weight: 600;">void</span> <span class="nf" style="color: #900; font-weight: 600;">parse_sequencing_summary</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">filename</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;">m<span class="idiff left right">ultim</span>ap</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;">out_map</span><span class="p">)</span></span>
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160
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<pre style="margin: 0;"> <span id="LC160" class="line" lang="cpp"><span class="p">{</span></span>
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165
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161
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<pre style="margin: 0;"> <span id="LC161" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// open</span></span>
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166
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<pre style="margin: 0;"> <span id="LC162" 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;">ifstream</span> <span class="n" style="color: #333;">in_file</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="203" style="width: 35px; color: rgba(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="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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -203,7 +199,7 @@ void parse_sequencing_summary(const std::string& filename, std::map<std::string,</td>
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203
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199
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<pre style="margin: 0;"> <span id="LC199" class="line" lang="cpp"> <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;">line</span><span class="p">,</span> <span class="sc" style="color: #d14;">'\t'</span><span class="p">);</span></span>
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204
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<pre style="margin: 0;"> <span id="LC200" 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;">fast5_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;">filename_idx</span><span class="p">];</span></span>
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205
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201
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<pre style="margin: 0;"> <span id="LC201" 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;">fields</span><span class="p">[</span><span class="n" style="color: #333;">read_name_idx</span><span class="p">];</span></span>
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206
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<pre style="margin: 0;">-<span id="LC206" class="line" lang="cpp"> <span class="n" style="color: #333;">out_map</span><span class="p"><span class="idiff left">[</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_filename</span></span><span class="p"><span class="idiff">]</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">read_name</span></span><span class="p">;</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="cpp"> <span class="n" style="color: #333;">out_map</span><span class="p"><span class="idiff left">.</span></span><span class="n" style="color: #333;"><span class="idiff">insert</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">std</span></span><span class="o" style="font-weight: 600;"><span class="idiff">::</span></span><span class="n" style="color: #333;"><span class="idiff">make_pair</span></span><span class="p"><span class="idiff">(</span></span><span class="n" style="color: #333;"><span class="idiff">fast5_filename</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff">read_name</span></span><span class="p"><span class="idiff right">))</span>;</span></span>
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<pre style="margin: 0;"> <span id="LC203" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC204" class="line" lang="cpp"><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC205" class="line" lang="cpp"></span>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -279,7 +275,7 @@ int index_main(int argc, char** argv)</td>
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<pre style="margin: 0;"> <span id="LC275" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// Read a map from fast5 files to read name from the sequencing summary files (if any)</span></span>
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="n" style="color: #333;">process_summary_fofn</span><span class="p">();</span></span>
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<pre style="margin: 0;">-<span id="LC282" 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="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;">fast5_to_read_name_map</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC278" 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;">m<span class="idiff left right">ultim</span>ap</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;">fast5_to_read_name_map</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC279" 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;">ss_filename</span> <span class="o" style="font-weight: 600;">:</span> <span class="n" style="color: #333;">opt</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">sequencing_summary_files</span><span class="p">)</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;">if</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;">verbose</span> <span class="o" style="font-weight: 600;">></span> <span class="mi" style="color: #099;">2</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;">fprintf</span><span class="p">(</span><span class="n" style="color: #333;">stderr</span><span class="p">,</span> <span class="s" style="color: #d14;">"summary: %s</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;">ss_filename</span><span class="p">.</span><span class="n" style="color: #333;">c_str</span><span class="p">());</span></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/commit/7868af613b689fbb895f987c5608a25cb8c32549#3e7589d9f810f7643a9b0d6c2e885784173011a1"><strong>src/nanopolish_polya_estimator.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">@@ -220,15 +220,21 @@ private:</td>
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<pre style="margin: 0;"> <span id="LC220" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// T -> T (100%)</span></span>
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<pre style="margin: 0;"> <span id="LC221" class="line" lang="cpp"> <span class="p">{</span><span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">1.00</span><span class="n" style="color: #333;">f</span><span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC222" class="line" lang="cpp"> <span class="p">};</span></span>
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<pre style="margin: 0;">-<span id="LC223" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">50/50 chance of starting on L or S</span></span></span>
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<pre style="margin: 0;">-<span id="LC224" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">start_probs</span><span class="p">[</span><span class="n" style="color: #333;">HMM_NUM_STATES</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="mf" style="color: #099;"><span class="idiff left">0.50</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">0.5</span>0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span> <span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// <span class="idiff left right">All state sequences must start on S:</span></span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">start_probs</span><span class="p">[</span><span class="n" style="color: #333;">HMM_NUM_STATES</span><span class="p">]</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span> <span class="mf" style="color: #099;"><span class="idiff left">1.00</span></span><span class="n" style="color: #333;"><span class="idiff">f</span></span><span class="p"><span class="idiff">,</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff right">0.0</span>0</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">0.00</span><span class="n" style="color: #333;">f</span> <span class="p">};</span></span>
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<pre style="margin: 0;"> <span id="LC225" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC226" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ----- emission parameters:</span></span>
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<pre style="margin: 0;"> <span id="LC227" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// emission parameters, from empirical MLE on manually-flagged reads:</span></span>
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<pre style="margin: 0;">-<span id="LC228" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// START, LEADER, and POLYA have Gaussian emissions;</span></span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// START has a mixture of Gaussian and Uniform emissions;</span></span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// LEADER and POLYA have Gaussian emissions;</span></span>
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<pre style="margin: 0;"> <span id="LC230" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// ADAPTER, TRANSCRIPT have Gaussian mixture emissions;</span></span>
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<pre style="margin: 0;"> <span id="LC231" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// CLIFF has Uniform emissions.</span></span>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="cpp"> <span class="n" style="color: #333;">GaussianParameters</span> <span class="n" style="color: #333;">s_emission</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mf" style="color: #099;">70.2737</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">3.7743</span><span class="n" style="color: #333;">f</span><span class="p">};</span></span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">s_begin</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">40.0</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">s_end</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">250.0</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="235" 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">
235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">s_prob</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.00476</span><span class="n" style="color: #333;">f</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">// == {1. / (250.0f - 40.0f)}</span></span>
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<td class="diff-line-num new new_line" data-linenumber="236" 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">
236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">s_norm_coeff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.50</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="237" 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">
237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">s_unif_coeff</span> <span class="o" style="font-weight: 600;">=</span> <span class="mf" style="color: #099;">0.50</span><span class="n" style="color: #333;">f</span><span class="p">;</span></span>
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232
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238
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="cpp"> <span class="n" style="color: #333;">GaussianParameters</span> <span class="n" style="color: #333;">l_emission</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mf" style="color: #099;">110.973</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">5.237</span><span class="n" style="color: #333;">f</span><span class="p">};</span></span>
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233
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239
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="cpp"> <span class="n" style="color: #333;">GaussianParameters</span> <span class="n" style="color: #333;">a0_emission</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mf" style="color: #099;">79.347</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">8.3702</span><span class="n" style="color: #333;">f</span><span class="p">};</span></span>
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234
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240
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="cpp"> <span class="n" style="color: #333;">GaussianParameters</span> <span class="n" style="color: #333;">a1_emission</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">{</span><span class="mf" style="color: #099;">63.3126</span><span class="n" style="color: #333;">f</span><span class="p">,</span> <span class="mf" style="color: #099;">2.7464</span><span class="n" style="color: #333;">f</span><span class="p">};</span></span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="271" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -265,7 +271,8 @@ private:</td>
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265
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271
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<pre style="margin: 0;"> <span id="LC271" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">log_probs</span><span class="p">;</span></span>
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266
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<pre style="margin: 0;"> <span id="LC272" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">HMM_START</span><span class="p">)</span> <span class="p">{</span></span>
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267
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<pre style="margin: 0;"> <span id="LC273" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// START state:</span></span>
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268
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<pre style="margin: 0;">-<span id="LC268" class="line" lang="cpp"> <span class="n" style="color: #333;">log_probs</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">log_normal_pdf</span><span class="p">(</span><span class="n" style="color: #333;">xx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s_emission</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">float</span> <span class="n" style="color: #333;">norm_term</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">s_norm_coeff</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">normal_pdf</span><span class="p">(</span><span class="n" style="color: #333;">xx</span><span class="p">,</span> <span class="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">s_emission</span><span class="p">);</span></span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="cpp"> <span class="n" style="color: #333;">log_probs</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;">log</span><span class="p">(</span><span class="n" style="color: #333;">norm_term</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">s_unif_coeff</span> <span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333;">s_prob</span><span class="p">);</span></span>
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269
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<pre style="margin: 0;"> <span id="LC276" class="line" lang="cpp"> <span class="p">}</span></span>
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270
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277
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<pre style="margin: 0;"> <span id="LC277" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">state</span> <span class="o" style="font-weight: 600;">==</span> <span class="n" style="color: #333;">HMM_LEADER</span><span class="p">)</span> <span class="p">{</span></span>
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271
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<pre style="margin: 0;"> <span id="LC278" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// LEADER state:</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="680" style="width: 35px; color: rgba(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="687" style="width: 35px; color: rgba(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">@@ -680,14 +687,13 @@ std::string pre_segmentation_qc(uint32_t suffix_clip, uint32_t prefix_clip, doub</td>
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680
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687
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<pre style="margin: 0;"> <span id="LC687" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">// These tests indicate that something went wrong in the segmentation algorithm.</span></span>
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681
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688
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<pre style="margin: 0;"> <span id="LC688" 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;">post_segmentation_qc</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">Segmentation</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">region_indices</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">SquiggleRead</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">sr</span><span class="p">)</span></span>
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682
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689
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<pre style="margin: 0;"> <span id="LC689" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">-<span id="LC683" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fetch sizes of LEADER, ADAPTER, POLYA regions:</span></span>
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<pre style="margin: 0;">-<span id="LC684" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">num_leader_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region_indices</span><span class="p">.</span><span class="n" style="color: #333;">leader</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// fetch sizes of ADAPTER and POLYA regions:</span></span>
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<pre style="margin: 0;"> <span id="LC691" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">num_adapter_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">(</span><span class="n" style="color: #333;">region_indices</span><span class="p">.</span><span class="n" style="color: #333;">adapter</span><span class="o" style="font-weight: 600;">+</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">region_indices</span><span class="p">.</span><span class="n" style="color: #333;">leader</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC692" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">double</span> <span class="n" style="color: #333;">num_polya_samples</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">region_indices</span><span class="p">.</span><span class="n" style="color: #333;">polya</span> <span class="o" style="font-weight: 600;">-</span> <span class="p">(</span><span class="n" style="color: #333;">region_indices</span><span class="p">.</span><span class="n" style="color: #333;">adapter</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="LC693" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC694" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">// check for NOREGION:</span></span>
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<pre style="margin: 0;"> <span id="LC695" 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;">qc_tag</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC690" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_<span class="idiff left">leader_samples</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff"><</span></span><span class="idiff"> </span><span class="mf" style="color: #099;"><span class="idiff">200.0</span></span><span class="idiff"> </span><span class="o" style="font-weight: 600;"><span class="idiff">||</span></span><span class="idiff"> </span><span class="n" style="color: #333;"><span class="idiff right">num_</span>adapter_samples</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">200.0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">num_polya_samples</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">200.0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="n" style="color: #333;">num_adapter_samples</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">200.0</span> <span class="o" style="font-weight: 600;">||</span> <span class="n" style="color: #333;">num_polya_samples</span> <span class="o" style="font-weight: 600;"><</span> <span class="mf" style="color: #099;">200.0</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC697" class="line" lang="cpp"> <span class="n" style="color: #333;">qc_tag</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"NOREGION"</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC698" 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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<pre style="margin: 0;"> <span id="LC699" class="line" lang="cpp"> <span class="n" style="color: #333;">qc_tag</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"PASS"</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">@@ -733,6 +739,11 @@ void estimate_polya_for_single_read(const ReadDB& read_db,</td>
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<pre style="margin: 0;"> <span id="LC739" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">region_start</span><span class="p">,</span></span>
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<pre style="margin: 0;"> <span id="LC740" class="line" lang="cpp"> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">region_end</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC741" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//----- check if primary or secondary alignment by inspecting FLAG; skip read if secondary:</span></span>
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<pre style="margin: 0;">+<span id="LC743" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">if</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;">flag</span> <span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">BAM_FSECONDARY</span><span class="p">)</span> <span class="p">{</span></span>
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="cpp"> <span class="k" style="font-weight: 600;">return</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="cpp"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC747" class="line" lang="cpp"> <span class="c1" style="color: #998; font-style: italic;">//----- load a squiggle read:</span></span>
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<pre style="margin: 0;"> <span id="LC748" 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="LC749" 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="p">(</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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