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GitLab

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<h3>

Andreas Tille pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/58b172b339ac772ee82bea1a0823da3132f8f706">58b172b3</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-12-01T08:12:52+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Really drop libbiosoup headers by removing the patch

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/1a3abaae04026aa113e5a72ce1aa6311ac9b4c90">1a3abaae</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-12-01T08:22:40+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Do not try to install biosoup

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/d791aa0d84f92ab789daf295d1f49f0fcd87bac2">d791aa0d</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-12-01T08:35:33+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Install cmake files to /usr/share/cmake to reflect the Architecture: all nature of the package

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbioparser-dev/-/commit/b36af389919113ce7da1248b6801e2a9ba783406">b36af389</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2021-12-01T08:36:23+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable

</pre>

</li>

</ul>

<h4>5 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">

debian/install

</a>

</li>

<li class="file-stats">

<a href="#8906dd7a4c756e6a5727e230190472b9f631c972">

<span class="deleted-file">

−

debian/patches/biosoup

</span>

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<span class="deleted-file">

−

debian/patches/series

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

debian/rules

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/e2222d604033ec469ab8ace1995bf1f12bfcf7fb...b36af389919113ce7da1248b6801e2a9ba783406#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libbioparser-dev (3.0.15-2) unstable; urgency=medium</span>

</pre>

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2

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

</pre>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Really drop libbiosoup headers by removing the patch</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">    Closes: #1000856</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Install cmake files to /usr/share/cmake to reflect the Architecture: all</span>

</pre>

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6

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">    nature of the package</span>

</pre>

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7

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

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Wed, 01 Dec 2021 08:35:40 +0100</span>

</pre>

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

</pre>

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1

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">libbioparser-dev (3.0.15-1) unstable; urgency=medium</span>

</pre>

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2

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

</pre>

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3

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">  [ Michael R. Crusoe ]</span>

</pre>

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<br>

</li>

<li id="68d8c5c6babbf5cf109b2584c454449dbff75772">

<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/e2222d604033ec469ab8ace1995bf1f12bfcf7fb...b36af389919113ce7da1248b6801e2a9ba783406#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>

<hr>

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1

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

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">include       usr</span></pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">vendor/biosoup/include usr</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8906dd7a4c756e6a5727e230190472b9f631c972">

<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/e2222d604033ec469ab8ace1995bf1f12bfcf7fb...b36af389919113ce7da1248b6801e2a9ba783406#8906dd7a4c756e6a5727e230190472b9f631c972"><strong>debian/patches/biosoup</strong>

deleted

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1

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: snapshot of https://github.com/rvaser/biosoup/tree/4be6880b62a8e9fc2322ede3f69f82384f99499e</span></span>

</pre>

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2

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>

</pre>

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3

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

4

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

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

<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbioparser-dev/vendor/biosoup/CMakeLists.txt</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="5" 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">

5

</td>

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

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

<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="p">@@ -0,0 +1,33 @@</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

6

</td>

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

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

<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+cmake_minimum_required(VERSION 3.9)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="7" 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">

7

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="8" 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">

8

</td>

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

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

<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+project(biosoup VERSION 0.8.1</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="9" 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">

9

</td>

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

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

<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                LANGUAGES CXX</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

10

</td>

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

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

<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                DESCRIPTION "Biosoup is a c++ collection of header only data structures used for storage and logging in bioinformatics tools.")</span></span>

</pre>

</td>

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

11

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="12" 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">

12

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wall -Wextra -pedantic")</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

13

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(CMAKE_CXX_STANDARD 11)</span></span>

</pre>

</td>

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

14

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(CMAKE_CXX_STANDARD_REQUIRED ON)</span></span>

</pre>

</td>

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

15

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(CMAKE_CXX_EXTENSIONS OFF)</span></span>

</pre>

</td>

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

16

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

</td>

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

<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

17

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

</td>

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

<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="18" 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">

18

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

</td>

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/lib)</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

19

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${PROJECT_BINARY_DIR}/bin)</span></span>

</pre>

</td>

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

<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

20

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

</tr>

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

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

21

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+add_library(${PROJECT_NAME} INTERFACE)</span></span>

</pre>

</td>

</tr>

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

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

22

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

</tr>

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

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

23

</td>

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

</td>

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+target_include_directories(${PROJECT_NAME} INTERFACE</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  $<BUILD_INTERFACE:${CMAKE_CURRENT_SOURCE_DIR}/include>)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+option(biosoup_build_tests "Build biosoup unit tests" OFF)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+if (biosoup_build_tests)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  find_package(GTest REQUIRED)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  add_executable(${PROJECT_NAME}_test</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    test/nucleic_acid_test.cpp</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    test/overlap_test.cpp</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    test/progress_bar_test.cpp</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    test/sequence_test.cpp</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    test/timer_test.cpp)</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  target_link_libraries(${PROJECT_NAME}_test</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="36" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC36" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    ${PROJECT_NAME}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="37" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    GTest::Main)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="38" 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="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+endif ()</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbioparser-dev/vendor/biosoup/include/biosoup/sequence.hpp</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="41" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC41" class="line" lang="diff"><span class="p">@@ -0,0 +1,89 @@</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Copyright (c) 2020 Robert Vaser</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="43" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifndef BIOSOUP_SEQUENCE_HPP_</span></span>

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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define BIOSOUP_SEQUENCE_HPP_</span></span>

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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <algorithm></span></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <atomic></span></span>

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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <cctype></span></span>

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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <cstdint></span></span>

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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <string></span></span>

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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+namespace biosoup {</span></span>

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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+struct Sequence {</span></span>

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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public:</span></span>

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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Sequence() = default;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Sequence(const std::string& name, const std::string& data)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      : Sequence(name.c_str(), name.size(), data.c_str(), data.size()) {}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Sequence(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const char* name, std::uint32_t name_len,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const char* data, std::uint32_t data_len)</span></span>

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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      : id(num_objects++),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        name(name, name_len),</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        data(data, data_len),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        quality() {}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Sequence(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const std::string& name,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const std::string& data,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const std::string& quality)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      : Sequence(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          name.c_str(), name.size(),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="76" 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="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          data.c_str(), data.size(),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="77" 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="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          quality.c_str(), quality.size()) {}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Sequence(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const char* name, std::uint32_t name_len,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const char* data, std::uint32_t data_len,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="82" 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="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const char* quality, std::uint32_t quality_len)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      : id(num_objects++),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="84" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        name(name, name_len),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        data(data, data_len),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="86" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        quality(quality, quality_len) {}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="87" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="88" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Sequence(const Sequence&) = default;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="89" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Sequence& operator=(const Sequence&) = default;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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

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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Sequence(Sequence&&) = default;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="92" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Sequence& operator=(Sequence&&) = default;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  ~Sequence() = default;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  void ReverseAndComplement() {  // (optional) Watson-Crick base pairing</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    for (auto& it : data) {</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="98" 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="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      switch (static_cast<char>(std::toupper(static_cast<unsigned char>(it)))) {</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="99" 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="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'A': it = 'T'; break;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'C': it = 'G'; break;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="101" 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="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'G': it = 'C'; break;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="102" 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="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'T': case 'U': it = 'A'; break;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="103" 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">

103

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'R': it = 'Y'; break;  // A || G</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="104" 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="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'Y': it = 'R'; break;  // C || T (U)</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'K': it = 'M'; break;  // G || T (U)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="106" 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">

106

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'M': it = 'K'; break;  // A || C</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="107" 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">

107

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'S': break;  // C || G</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="108" 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">

108

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'W': break;  // A || T (U)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="109" 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">

109

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'B': it = 'V'; break;  // !A</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="110" 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">

110

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'D': it = 'H'; break;  // !C</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="111" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

111

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

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<pre style="margin: 0;">-<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'H': it = 'D'; break;  // !G</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="112" 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">

112

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        case 'V': it = 'B'; break;  // !T (!U)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="113" 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">

113

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<td class="new_line diff-line-num old" data-linenumber="0" 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="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        default: break;  // N || -</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="114" 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">

114

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<pre style="margin: 0;">-<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="115" 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">

115

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<pre style="margin: 0;">-<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="116" 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">

116

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<pre style="margin: 0;">-<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    std::reverse(data.begin(), data.end());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="117" 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">

117

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<pre style="margin: 0;">-<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+    std::reverse(quality.begin(), quality.end());</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="118" 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">

118

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

<pre style="margin: 0;">-<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  }</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="119" 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">

119

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

<pre style="margin: 0;">-<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="120" 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">

120

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<pre style="margin: 0;">-<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  static std::atomic<std::uint32_t> num_objects;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="121" 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">

121

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</td>

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

<pre style="margin: 0;">-<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

</td>

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<td class="old_line diff-line-num old" data-linenumber="122" 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">

122

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<pre style="margin: 0;">-<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::uint32_t id;  // (optional) initialize num_objects to 0</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="123" 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">

123

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<pre style="margin: 0;">-<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::string name;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="124" 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">

124

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<pre style="margin: 0;">-<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::string data;</span></span>

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<pre style="margin: 0;">-<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::string quality;  // (optional) Phred quality scores</span></span>

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<pre style="margin: 0;">-<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+};</span></span>

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<pre style="margin: 0;">-<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}  // namespace biosoup</span></span>

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<pre style="margin: 0;">-<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif  // BIOSOUP_SEQUENCE_HPP_</span></span>

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<pre style="margin: 0;">-<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- /dev/null</span></span>

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<pre style="margin: 0;">-<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbioparser-dev/vendor/biosoup/include/biosoup/overlap.hpp</span></span>

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<pre style="margin: 0;">-<span id="LC133" class="line" lang="diff"><span class="p">@@ -0,0 +1,80 @@</span></span>

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<pre style="margin: 0;">-<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+// Copyright (c) 2020 Robert Vaser</span></span>

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<pre style="margin: 0;">-<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#ifndef BIOSOUP_OVERLAP_HPP_</span></span>

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<pre style="margin: 0;">-<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#define BIOSOUP_OVERLAP_HPP_</span></span>

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<pre style="margin: 0;">-<span id="LC138" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <cstdint></span></span>

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<pre style="margin: 0;">-<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#include <string></span></span>

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<pre style="margin: 0;">-<span id="LC141" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+namespace biosoup {</span></span>

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<pre style="margin: 0;">-<span id="LC143" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

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<pre style="margin: 0;">-<span id="LC144" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+struct Overlap {</span></span>

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<pre style="margin: 0;">-<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public:</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Overlap() = default;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Overlap(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="149" 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="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      std::uint64_t lhs_id, std::uint32_t lhs_begin, std::uint32_t lhs_end,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      std::uint64_t rhs_id, std::uint32_t rhs_begin, std::uint32_t rhs_end,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      std::uint32_t score,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="152" 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="LC152" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      bool strand = true)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="153" 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="LC153" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      : lhs_id(lhs_id),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC154" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        lhs_begin(lhs_begin),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="155" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        lhs_end(lhs_end),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC156" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        rhs_id(rhs_id),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="157" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC157" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        rhs_begin(rhs_begin),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="158" 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="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        rhs_end(rhs_end),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="159" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC159" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        score(score),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="160" 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="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        strand(strand),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="161" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        alignment() {}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Overlap(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="164" 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="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      std::uint64_t lhs_id, std::uint32_t lhs_begin, std::uint32_t lhs_end,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      std::uint64_t rhs_id, std::uint32_t rhs_begin, std::uint32_t rhs_end,</span></span>

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<pre style="margin: 0;">-<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      std::uint32_t score,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="167" 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="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const std::string& alignment,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="168" 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="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      bool strand = true)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="169" 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="LC169" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      : Overlap(</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="170" 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="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          lhs_id, lhs_begin, lhs_end,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          rhs_id, rhs_begin, rhs_end,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC172" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          score,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="173" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC173" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          alignment.c_str(), alignment.size(),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="174" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC174" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+          strand) {}</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Overlap(</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC177" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      std::uint64_t lhs_id, std::uint32_t lhs_begin, std::uint32_t lhs_end,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      std::uint64_t rhs_id, std::uint32_t rhs_begin, std::uint32_t rhs_end,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      std::uint32_t score,</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="180" 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="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      const char* alignment, std::uint32_t alignment_len,</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC181" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      bool strand = true)</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="182" 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="LC182" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+      : lhs_id(lhs_id),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC183" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        lhs_begin(lhs_begin),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="184" 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="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        lhs_end(lhs_end),</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        rhs_id(rhs_id),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="186" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC186" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        rhs_begin(rhs_begin),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="187" 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="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        rhs_end(rhs_end),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="188" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC188" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        score(score),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="189" 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">

189

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<pre style="margin: 0;">-<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        strand(strand),</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="190" 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">

190

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<pre style="margin: 0;">-<span id="LC190" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+        alignment(alignment, alignment_len) {}</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="191" 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="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="192" 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="LC192" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Overlap(const Overlap&) = default;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="193" 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="LC193" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Overlap& operator=(const Overlap&) = default;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="194" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

194

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<pre style="margin: 0;">-<span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="195" 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="LC195" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Overlap(Overlap&&) = default;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="196" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC196" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  Overlap& operator=(Overlap&&) = default;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="197" 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="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="198" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  ~Overlap() = default;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="199" 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="LC199" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="200" 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="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::uint32_t lhs_id;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="201" 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="LC201" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::uint32_t lhs_begin;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="202" 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="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::uint32_t lhs_end;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="203" 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="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::uint32_t rhs_id;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="204" 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="LC204" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::uint32_t rhs_begin;</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="205" 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="LC205" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::uint32_t rhs_end;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC206" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::uint32_t score;  // based on k-mer matches or alignment score</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  bool strand;  // (optional) Watson-Crick strand</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="208" 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="LC208" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  std::string alignment;  // (optional) cigar string</span></span>

</pre>

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209

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<pre style="margin: 0;">-<span id="LC209" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+};</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="210" 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">

210

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<pre style="margin: 0;">-<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="211" 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">

211

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<pre style="margin: 0;">-<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}  // namespace biosoup</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="212" 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="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>

</pre>

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<td class="old_line diff-line-num old" data-linenumber="213" 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">

213

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<pre style="margin: 0;">-<span id="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+#endif  // BIOSOUP_OVERLAP_HPP_</span></span></pre>

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</tr>

</table>

<br>

</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/e2222d604033ec469ab8ace1995bf1f12bfcf7fb...b36af389919113ce7da1248b6801e2a9ba783406#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong>

deleted

</a>

<hr>

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

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

1

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

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

<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">biosoup</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/libbioparser-dev/-/compare/e2222d604033ec469ab8ace1995bf1f12bfcf7fb...b36af389919113ce7da1248b6801e2a9ba783406#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,3 +14,8 @@ override_dh_auto_test:</td>

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<td class="old_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<td class="new_line diff-line-num" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

14

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>

</pre>

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<td class="old_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<td class="new_line diff-line-num" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">     set -e -x; for f in obj-*/bin/*_test; do [ ! -x $$f ] || $$f; done</span>

</pre>

</td>

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<td class="old_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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<td class="new_line diff-line-num" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

16

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">endif</span>

</pre>

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

</td>

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

17

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

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

</pre>

</td>

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

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

18

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

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

</pre>

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

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

19

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

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

</pre>

</td>

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

</td>

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

20

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

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">     mv debian/`dh_listpackages`/usr/lib/*/cmake debian/`dh_listpackages`/usr/share</span>

</pre>

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

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

21

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">     rm -rf debian/`dh_listpackages`/usr/lib</span></pre>

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