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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/adapterremoval">Debian Med / adapterremoval</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/adapterremoval/-/commit/dd439107c0050e20fdd33a2a5e06acbcc129e3ab">dd439107</a></strong>
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<span>by Andreas Tille</span>
<i>at 2022-04-15T15:44:08+02:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.3</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#43b6fe73a99e26d838cc62790847dc00d3d069db">
AdapterRemoval.1
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<li class="file-stats">
<a href="#7facec255884dc55d3818e4dfbea89b1bdd7f49e">
CHANGES.md
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<a href="#254a2da7a740675e537439eb88e32083b9ea4771">
docs/conf.py
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<a href="#a815e875b36e3d39931ecf171111b331c3bf8437">
src/main.hpp
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<li class="file-stats">
<a href="#2318bda8f6ed8d03d85eb1ce3d4c2feb04f8abc8">
tests/unit/catch.hpp
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<h4>Changes:</h4>
<li id="43b6fe73a99e26d838cc62790847dc00d3d069db">
<a href="https://salsa.debian.org/med-team/adapterremoval/-/commit/dd439107c0050e20fdd33a2a5e06acbcc129e3ab#43b6fe73a99e26d838cc62790847dc00d3d069db"><strong>AdapterRemoval.1</strong></a>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">.\" Man page generated from reStructuredText.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">.</span>
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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="LC3" class="line" lang="plaintext">.TH "ADAPTERREMOVAL" "1" "Mar 17, 2021" "2.3.0" "AdapterRemoval"</span>
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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="plaintext">.SH NAME</span>
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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="plaintext">AdapterRemoval \- Fast short-read adapter trimming and processing</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">.</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">.nr rst2man-indent-level 0</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">.</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,6 +27,9 @@ level margin: \\n[rst2man-indent\\n[rst2man-indent-level]]</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">.\" new: \\n[rst2man-indent\\n[rst2man-indent-level]]</span>
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<td class="old_line diff-line-num" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">.in \\n[rst2man-indent\\n[rst2man-indent-level]]u</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC29" class="line" lang="plaintext">..</span>
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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="LC30" class="line" lang="plaintext">.TH "ADAPTERREMOVAL" "1" "Apr 15, 2022" "2.3.3" "AdapterRemoval"</span>
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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="LC31" class="line" lang="plaintext">.SH NAME</span>
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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="LC32" class="line" lang="plaintext">AdapterRemoval \- Fast short-read adapter trimming and processing</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">.SH SYNOPSIS</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">.sp</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">\fBAdapterRemoval\fP [\fIoptions\fP\&...] \-\-file1 <\fIfilenames\fP> [\-\-file2 <\fIfilenames\fP>]</span>
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<li id="7facec255884dc55d3818e4dfbea89b1bdd7f49e">
<a href="https://salsa.debian.org/med-team/adapterremoval/-/commit/dd439107c0050e20fdd33a2a5e06acbcc129e3ab#7facec255884dc55d3818e4dfbea89b1bdd7f49e"><strong>CHANGES.md</strong></a>
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0"><pre style="margin: 0;">+<span id="LC1" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Version 2.3.3 - 2022-04-15</span></span>
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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="LC3" class="line" lang="markdown"><span class="p"> *</span> Updated Catch2 to fix compilation with glibc 2.34, courtesy of loganrosen. </span>
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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="LC4" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC5" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">### Version 2.3.2 - 2021-03-17</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown"><span class="p"> *</span> Improved error messages when AdapterRemoval failed to open or write FASTQ</span>
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<a href="https://salsa.debian.org/med-team/adapterremoval/-/commit/dd439107c0050e20fdd33a2a5e06acbcc129e3ab#254a2da7a740675e537439eb88e32083b9ea4771"><strong>docs/conf.py</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -54,9 +54,9 @@ author = u'Mikkel Schubert; Stinus Lindgreen'</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC54" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># built documents.</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC55" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC56" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The short X.Y version.</span></span>
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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="LC57" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'2.3.<span class="idiff left right deletion">2</span>'</span></span>
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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="LC57" class="line" lang="python"><span class="n" style="color: #333;">version</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'2.3.<span class="idiff left right addition">3</span>'</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC58" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The full version, including alpha/beta/rc tags.</span></span>
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<td class="new_line diff-line-num old" data-linenumber="59" 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="LC59" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'2.3.<span class="idiff left right deletion">2</span>'</span></span>
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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="LC59" class="line" lang="python"><span class="n" style="color: #333;">release</span> <span class="o" style="font-weight: 600;">=</span> <span class="sa">u</span><span class="s" style="color: #d14;">'2.3.<span class="idiff left right addition">3</span>'</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC60" class="line" lang="python"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC61" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># The language for content autogenerated by Sphinx. Refer to documentation</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC62" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;"># for a list of supported languages.</span></span>
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<a href="https://salsa.debian.org/med-team/adapterremoval/-/commit/dd439107c0050e20fdd33a2a5e06acbcc129e3ab#a815e875b36e3d39931ecf171111b331c3bf8437"><strong>src/main.hpp</strong></a>
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<td class="line_content match" style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -31,7 +31,7 @@ namespace ar</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC31" class="line" lang="cpp"><span class="p">{</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC32" class="line" lang="cpp"></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC33" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">NAME</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"AdapterRemoval"</span><span class="p">;</span></span>
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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="LC34" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ver. 2.3.<span class="idiff left right deletion">2</span>"</span><span class="p">;</span></span>
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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="LC34" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"ver. 2.3.<span class="idiff left right addition">3</span>"</span><span class="p">;</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC35" class="line" lang="cpp"><span class="k" style="font-weight: 600;">const</span> <span class="n" style="color: #333;">std</span><span class="o" style="font-weight: 600;">::</span><span class="n" style="color: #333;">string</span> <span class="n" style="color: #333;">HELPTEXT</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC36" class="line" lang="cpp"> <span class="s" style="color: #d14;">"This program searches for and removes remnant adapter sequences from</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;"><pre style="margin: 0;"> <span id="LC37" class="line" lang="cpp"> <span class="s" style="color: #d14;">"your read data. The program can analyze both single end and paired end</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;">"</span></span>
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<a href="https://salsa.debian.org/med-team/adapterremoval/-/commit/dd439107c0050e20fdd33a2a5e06acbcc129e3ab#2318bda8f6ed8d03d85eb1ce3d4c2feb04f8abc8"><strong>tests/unit/catch.hpp</strong></a>
The diff for this file was not included because it is too large.
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