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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/cat-bat">Debian Med / cat-bat</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/cat-bat/-/commit/c4dd24add4b76ad6038a8619d82f7f49f76e66dd">c4dd24ad</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-05-27T13:26:43+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.0.5</pre>
</li>
</ul>
<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#6fd8d419abb30b8ad718bd6afa3bf33bf27bae47">
CAT_pack/about.py
</a>
</li>
<li class="file-stats">
<a href="#e8222836be7fdb29f66b8b4d17f23b4258132af6">
CAT_pack/bins.py
</a>
</li>
<li class="file-stats">
<a href="#3bde2f4ee51ad9ed542735d302116cb0044e0701">
CAT_pack/check.py
</a>
</li>
<li class="file-stats">
<a href="#ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
CHANGELOG.md
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="6fd8d419abb30b8ad718bd6afa3bf33bf27bae47">
<a href="https://salsa.debian.org/med-team/cat-bat/-/commit/c4dd24add4b76ad6038a8619d82f7f49f76e66dd#6fd8d419abb30b8ad718bd6afa3bf33bf27bae47"><strong>CAT_pack/about.py</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">#!/usr/bin/env python3</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="n" style="color: #333;">__author__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'F. A. Bastiaan von Meijenfeldt'</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'5.0.<span class="idiff left right">4</span>'</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Ma<span class="idiff left right">rch 18</span>, 2020'</span></span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="python"><span class="n" style="color: #333;">__version__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'5.0.<span class="idiff left right">5</span>'</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="python"><span class="n" style="color: #333;">__date__</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">'Ma<span class="idiff left right">y 26</span>, 2020'</span></span></pre>
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<br>
</li>
<li id="e8222836be7fdb29f66b8b4d17f23b4258132af6">
<a href="https://salsa.debian.org/med-team/cat-bat/-/commit/c4dd24add4b76ad6038a8619d82f7f49f76e66dd#e8222836be7fdb29f66b8b4d17f23b4258132af6"><strong>CAT_pack/bins.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">@@ -236,6 +236,10 @@ def import_bins(bin_folder,</td>
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<pre style="margin: 0;"> <span id="LC236" class="line" lang="python">    <span class="n" style="color: #333;">contig_names</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">set</span><span class="p">()</span></span>
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<pre style="margin: 0;"> <span id="LC238" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">file_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">bin_folder</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Skip hidden files.</span></span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC243" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="n" style="color: #333;">bin_suffix</span><span class="p">):</span></span>
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<pre style="margin: 0;"> <span id="LC244" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC245" class="line" lang="python">        </span>
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<li id="3bde2f4ee51ad9ed542735d302116cb0044e0701">
<a href="https://salsa.debian.org/med-team/cat-bat/-/commit/c4dd24add4b76ad6038a8619d82f7f49f76e66dd#3bde2f4ee51ad9ed542735d302116cb0044e0701"><strong>CAT_pack/check.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">@@ -232,6 +232,10 @@ def check_bin_folder(bin_folder, bin_suffix, log_file, quiet):</td>
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<pre style="margin: 0;"> <span id="LC232" class="line" lang="python">    </span>
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<pre style="margin: 0;"> <span id="LC233" class="line" lang="python">    <span class="n" style="color: #333;">tmp</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">[]</span></span>
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<pre style="margin: 0;"> <span id="LC234" class="line" lang="python">    <span class="k" style="font-weight: 600;">for</span> <span class="n" style="color: #333;">file_</span> <span class="ow" style="font-weight: 600;">in</span> <span class="n" style="color: #333;">os</span><span class="p">.</span><span class="n" style="color: #333;">listdir</span><span class="p">(</span><span class="n" style="color: #333;">bin_folder</span><span class="p">):</span></span>
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<td class="diff-line-num new old_line" data-linenumber="235" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">startswith</span><span class="p">(</span><span class="s" style="color: #d14;">'.'</span><span class="p">):</span></span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="python">            <span class="c1" style="color: #998; font-style: italic;"># Skip hidden files.</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="python"></span>
</pre>
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<pre style="margin: 0;"> <span id="LC239" class="line" lang="python">        <span class="k" style="font-weight: 600;">if</span> <span class="ow" style="font-weight: 600;">not</span> <span class="n" style="color: #333;">file_</span><span class="p">.</span><span class="n" style="color: #333;">endswith</span><span class="p">(</span><span class="n" style="color: #333;">bin_suffix</span><span class="p">):</span></span>
</pre>
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<pre style="margin: 0;"> <span id="LC240" class="line" lang="python">            <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC241" class="line" lang="python"></span>
</pre>
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</li>
<li id="ab09011fa121d0a2bb9fa4ca76094f2482b902b7">
<a href="https://salsa.debian.org/med-team/cat-bat/-/commit/c4dd24add4b76ad6038a8619d82f7f49f76e66dd#ab09011fa121d0a2bb9fa4ca76094f2482b902b7"><strong>CHANGELOG.md</strong></a>
<hr>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="markdown"><span class="gh" style="color: #999;"># Changelog</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="2" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<td class="diff-line-num new new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 5.0.5.</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
</td>
<td class="diff-line-num new new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="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">Skip hidden files in bin folder.</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
 
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<td class="diff-line-num new new_line" data-linenumber="5" 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">
5
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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="LC5" class="line" lang="markdown"></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
3
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="markdown"><span class="gu" style="color: #800080; font-weight: 600;">## 5.0.4.</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
4
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="markdown">We have added the <span class="sb" style="color: #d14;">`--no_stars`</span> flag alongside a minor bug fix.</span>
</pre>
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