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<h3>
Steffen Möller pushed to branch master
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/33ce6e2884ff275b5bd030ccecc0e223b862de04">33ce6e28</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-03T19:25:11+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: New upstream version
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanopolish/-/commit/55e72c8dd14f1ea3aaab30db00cf33667602945d">55e72c8d</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-05-03T19:25:12+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.13.2</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanopolish/-/commit/96392884c31ad3589f178952f9af1916602ab908">96392884</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-05-03T19:25:24+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/0.13.2'
Update to upstream version '0.13.2'
with Debian dir 482bb7919af06178c32028d08ea7bef5d9edaff4</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/nanopolish/-/commit/6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7">6fa303ab</a></strong>
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<span>by Steffen Moeller</span>
<i>at 2020-05-03T19:28:45+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">routine-update: Ready to upload to unstable
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</li>
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<h4>6 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
README.md
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
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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="#dd987838388d2c42ef5e4897eaef047ea34a4426">
src/io/nanopolish_fast5_loader.cpp
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<li class="file-stats">
<a href="#244f2077b9e28a5e6394deda0b7574b0f80f501c">
src/nanopolish_squiggle_read.cpp
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</ul>
<h4>Changes:</h4>
<li id="8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d">
<a href="https://salsa.debian.org/med-team/nanopolish/-/compare/61a7441722fc79f59acf8db2ad0b19ee45f2a40a...6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7#8ec9a00bfd09b3190ac6b22251dbb1aa95a0579d"><strong>README.md</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -6,6 +6,8 @@ Software package for signal-level analysis of Oxford Nanopore sequencing data. N</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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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="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## Release notes</span></span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC8" class="line" lang="markdown"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="markdown"><span class="p">*</span> 0.13.2: fix memory leak when loading signal data</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="markdown"><span class="p">*</span> 0.13.1: fix <span class="sb" style="color: #d14;">`nanopolish index`</span> performance issue for some barcoding runs</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="markdown"></span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="markdown"><span class="p">*</span> 0.13.0: modify HMM transitions to allow the balance between insertions and deletions to be changed depending on mode (consensus vs reference variants)</span>
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<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/nanopolish/-/compare/61a7441722fc79f59acf8db2ad0b19ee45f2a40a...6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">nanopolish (0.13.<span class="idiff left right">1-1) UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">nanopolish (0.13.<span class="idiff left right">2-1) unstable</span>; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> [ Michael R. Crusoe ]</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * New upstream version</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Enable building anywhere, there are no longer any SIMD intrinsics</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> -- <span class="idiff left right">Michael R. Crusoe <michael.crusoe@gmail.com> Thu, 23 Apr 2020 13:48:28</span> +0200</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- <span class="idiff left right">Steffen Moeller <moeller@debian.org> Sun, 03 May 2020 19:25:27</span> +0200</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">nanopolish (0.12.1-2) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/-/compare/61a7441722fc79f59acf8db2ad0b19ee45f2a40a...6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 12),</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> libfast5-dev (>= 0.6.5),</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> libhts-dev,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> libeigen3-dev,</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext"> libminimap2-dev<span class="idiff left right"> (>= 2.17+dfsg-8)</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> libminimap2-dev</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/nanopolish</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/nanopolish.git</span>
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<a href="https://salsa.debian.org/med-team/nanopolish/-/compare/61a7441722fc79f59acf8db2ad0b19ee45f2a40a...6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7#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="cpp"><span class="cp" style="color: #999; font-weight: 600;">#include "logsum.h"</span></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_NAME "nanopolish"</span></span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "0.13.<span class="idiff left right">1</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_VERSION "0.13.<span class="idiff left right">2</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="cpp"><span class="cp" style="color: #999; font-weight: 600;">#define PACKAGE_BUGREPORT "https://github.com/jts/nanopolish/issues"</span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="cpp"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="c1" style="color: #998; font-style: italic;">//</span></span>
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<a href="https://salsa.debian.org/med-team/nanopolish/-/compare/61a7441722fc79f59acf8db2ad0b19ee45f2a40a...6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7#dd987838388d2c42ef5e4897eaef047ea34a4426"><strong>src/io/nanopolish_fast5_loader.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">@@ -24,6 +24,9 @@ Fast5Loader::~Fast5Loader()</td>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="cpp"><span class="n" style="color: #333;">Fast5Data</span> <span class="n" style="color: #333;">Fast5Loader</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">load_read</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="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;">read_name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="cpp"><span class="p">{</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="cpp"> <span class="n" style="color: #333;">Fast5Data</span> <span class="n" style="color: #333;">data</span><span class="p">;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="cpp"> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">rt</span><span class="p">.</span><span class="n" style="color: #333;">n</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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<td class="diff-line-num new new_line" data-linenumber="28" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="cpp"> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">rt</span><span class="p">.</span><span class="n" style="color: #333;">raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="cpp"></span>
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27
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="cpp"> <span class="n" style="color: #333;">fast5_file</span> <span class="n" style="color: #333;">f5_file</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">fast5_open</span><span class="p">(</span><span class="n" style="color: #333;">filename</span><span class="p">);</span></span>
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28
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31
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<pre style="margin: 0;"> <span id="LC31" 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_is_open</span><span class="p">(</span><span class="n" style="color: #333;">f5_file</span><span class="p">))</span> <span class="p">{</span></span>
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29
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">is_valid</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">false</span><span class="p">;</span></span>
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<li id="244f2077b9e28a5e6394deda0b7574b0f80f501c">
<a href="https://salsa.debian.org/med-team/nanopolish/-/compare/61a7441722fc79f59acf8db2ad0b19ee45f2a40a...6fa303abb77cb1bc622aef3c3e45f4c9b48b5bd7#244f2077b9e28a5e6394deda0b7574b0f80f501c"><strong>src/nanopolish_squiggle_read.cpp</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="88" style="width: 35px; color: rgba(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="88" style="width: 35px; color: rgba(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">@@ -88,6 +88,8 @@ SquiggleRead::SquiggleRead(const std::string& name, const ReadDB& read_db, const</td>
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88
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88
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<pre style="margin: 0;"> <span id="LC88" 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="k" style="font-weight: 600;">this</span><span class="o" style="font-weight: 600;">-></span><span class="n" style="color: #333;">events</span><span class="p">[</span><span class="mi" style="color: #099;">0</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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89
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89
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="cpp"> <span class="n" style="color: #333;">assert</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;">base_model</span><span class="p">[</span><span class="mi" style="color: #099;">0</span><span class="p">]</span> <span class="o" style="font-weight: 600;">!=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">);</span></span>
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90
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90
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="cpp"> <span class="p">}</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="cpp"> <span class="n" style="color: #333;">free</span><span class="p">(</span><span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">rt</span><span class="p">.</span><span class="n" style="color: #333;">raw</span><span class="p">);</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="cpp"> <span class="n" style="color: #333;">data</span><span class="p">.</span><span class="n" style="color: #333;">rt</span><span class="p">.</span><span class="n" style="color: #333;">raw</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">NULL</span><span class="p">;</span></span>
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91
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93
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<pre style="margin: 0;"> <span id="LC93" class="line" lang="cpp"><span class="p">}</span></span>
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92
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94
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<pre style="margin: 0;"> <span id="LC94" class="line" lang="cpp"></span>
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93
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<pre style="margin: 0;"> <span id="LC95" class="line" lang="cpp"><span class="n" style="color: #333;">SquiggleRead</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">SquiggleRead</span><span class="p">(</span><span class="k" style="font-weight: 600;">const</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;">Fast5Data</span><span class="o" style="font-weight: 600;">&</span> <span class="n" style="color: #333;">data</span><span class="p">,</span> <span class="k" style="font-weight: 600;">const</span> <span class="kt" style="color: #458; font-weight: 600;">uint32_t</span> <span class="n" style="color: #333;">flags</span><span class="p">)</span></span>
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