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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/plasmidid">Debian Med / plasmidid</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/plasmidid/-/commit/4d18b933c6acd8426f2d05baa0218b584bbe9f12">4d18b933</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-26T22:38:51+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Remove empty patch
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plasmidid/-/commit/a19e15460cf6bf59f9a5de40b839cf107565c48f">a19e1546</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-26T22:50:35+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plasmidid/-/commit/84c790eea46e335a2f054b653f57426d4c8ed2ef">84c790ee</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-26T22:55:01+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add missing comma
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plasmidid/-/commit/6a488173a876e0a35b5d7ebc4285ad74f455b922">6a488173</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-26T23:02:46+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fix spelling
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/plasmidid/-/commit/1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9">1af39f1b</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2020-06-26T23:05:40+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to new
</pre>
</li>
</ul>
<h4>7 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#a91884b6840a0818132e75dee05dae7335f90528">
debian/patches/AdjustPythonPath.patch
</a>
</li>
<li class="file-stats">
<a href="#8daca342044415c3c42946d456d929e90f72f221">
<span class="deleted-file">
−
debian/patches/config_files.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#5ed2b78a31077735f59465c1b69dcbf181908700">
debian/patches/fixTests.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6">
<span class="new-file">
+
debian/patches/spelling.patch
</span>
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/plasmidid/-/compare/c218fc2844b214418a589bba99b80bd743115a7b...1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">plasmidid (1.6.3+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="1" 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="LC1" class="line" lang="plaintext">plasmidid (1.6.3+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
</pre>
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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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<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="diff-line-num new_line old" data-linenumber="3" 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="plaintext"> [ Andreas Tille ]</span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #963758)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num old old_line" 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">
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> [ Steffen Moeller ]</span>
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<td class="diff-line-num old old_line" 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">
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> * debhelper-compat 13 (routine-update)</span>
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<td class="diff-line-num old old_line" 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">
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"> * Rules-Requires-Root: no (routine-update)</span>
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<td class="diff-line-num old old_line" 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">
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<td class="diff-line-num new_line 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">
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="plaintext"> * Set upstream metadata fields: Bug-Database, Bug-Submit, Repository,</span>
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<td class="diff-line-num old old_line" 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">
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> Repository-Browse. (routine-update)</span>
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<td class="diff-line-num old old_line" 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">
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext"> * Employ help2man to create missing man page</span>
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<td class="diff-line-num old_line" data-linenumber="12" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="diff-line-num new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> * Tests fail, apparently because of prokka</span>
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<td class="diff-line-num old_line" data-linenumber="13" 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="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="plaintext"> https://github.com/BU-ISCIII/plasmidID/issues/12</span>
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<td class="diff-line-num 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">
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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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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/plasmidid/-/compare/c218fc2844b214418a589bba99b80bd743115a7b...1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -7,7 +7,7 @@ Priority: optional</td>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">Build-Depends: debhelper-compat (= 13),</span>
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<td class="diff-line-num new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext"> dh-python,</span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext"> python3-all,</span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext"> help2man</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> help2man<span class="idiff left right">,</span></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> ncbi-blast+ <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> bedtools <!nocheck>,</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> bowtie2 <!nocheck>,</span>
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<a href="https://salsa.debian.org/med-team/plasmidid/-/compare/c218fc2844b214418a589bba99b80bd743115a7b...1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9#a91884b6840a0818132e75dee05dae7335f90528"><strong>debian/patches/AdjustPythonPath.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2020-06-26 18:33:35 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix Python3 path</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">Index: plasmidid/bin/download_plasmid_database.py</span>
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2
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- plasmidid.orig/bin/download_plasmid_database.py</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -8,13 +12,6 @@ Index: plasmidid/bin/download_plasmid_database.py</td>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> # Standard library imports</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="diff"> import os</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"><span class="p">@@ -157,4 +157,4 @@</span> if __name__ == '__main__':</span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"> main()</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> except Exception as e:</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"> logger.exception(e)</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise</span></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"><span class="gh" style="color: #999;">Index: plasmidid/bin/mashclust.py</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- plasmidid.orig/bin/mashclust.py</span></span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -25,13 +22,6 @@ Index: plasmidid/bin/mashclust.py</td>
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25
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22
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> </span>
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26
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> # Standard library imports</span>
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27
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> import os</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="p">@@ -396,4 +396,4 @@</span> if __name__ == '__main__':</span>
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29
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"> main()</span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"> except Exception as e:</span>
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31
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> logger.exception(e)</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise</span></span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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34
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ raise</span></span>
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35
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"><span class="gh" style="color: #999;">Index: plasmidid/bin/summary_report_pid.py</span></span>
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36
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26
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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37
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- plasmidid.orig/bin/summary_report_pid.py</span></span>
</pre>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="42" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -42,10 +32,3 @@ Index: plasmidid/bin/summary_report_pid.py</td>
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42
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32
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> </span>
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43
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33
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="diff"> # Standard library imports</span>
</pre>
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44
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="diff"> import os</span></pre>
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<pre style="margin: 0;">-<span id="LC45" class="line" lang="diff"><span class="p">@@ -465,4 +465,4 @@</span> if __name__ == '__main__':</span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="diff"> main()</span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"> except Exception as e:</span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"> logger.exception(e)</span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- raise</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</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;">+ raise</span></span></pre>
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<li id="8daca342044415c3c42946d456d929e90f72f221">
<a href="https://salsa.debian.org/med-team/plasmidid/-/compare/c218fc2844b214418a589bba99b80bd743115a7b...1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9#8daca342044415c3c42946d456d929e90f72f221"><strong>debian/patches/config_files.patch</strong>
deleted
</a>
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<li id="5ed2b78a31077735f59465c1b69dcbf181908700">
<a href="https://salsa.debian.org/med-team/plasmidid/-/compare/c218fc2844b214418a589bba99b80bd743115a7b...1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9#5ed2b78a31077735f59465c1b69dcbf181908700"><strong>debian/patches/fixTests.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Steffen Moeller</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: 2020-06-26 19:12:34 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Drop .sh extension of the binary</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">Index: plasmidid/TEST_DATA/test.sh</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gh" style="color: #999;">===================================================================</span></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- plasmidid.orig/TEST_DATA/test.sh</span></span>
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<a href="https://salsa.debian.org/med-team/plasmidid/-/compare/c218fc2844b214418a589bba99b80bd743115a7b...1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">config_files.patch</span>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">fixTests.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">AdjustPythonPath.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">spelling.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/plasmidid/-/compare/c218fc2844b214418a589bba99b80bd743115a7b...1af39f1b85e8ff8e28d734d25e7fe4fedb8ffbd9#45ae034d1d71b2d961abb7c91cf3d2f1a02a59c6"><strong>debian/patches/spelling.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 26 Jun 2020 23:02:03 +0200</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix spelling</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/README.md</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/README.md</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -137,15 +137,15 @@</span> usage : plasmidID <-1 R1> <-2 R2> <-d da</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> --no-trim Reads supplied will not be quality trimmed</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> Coverage and Clustering:</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -C | --coverage-cutoff <int> minimun coverage percentage to select a plasmid as scafold (0-100), default 80</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -S | --coverage-summary <int> minimun coverage percentage to include plasmids in summary image (0-100), default 90</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -C | --coverage-cutoff <int> minimum coverage percentage to select a plasmid as scafold (0-100), default 80</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -S | --coverage-summary <int> minimum coverage percentage to include plasmids in summary image (0-100), default 90</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> -f | --cluster <int> kmer identity to cluster plasmids into the same representative sequence (0 means identical) (0-1), default 0.5</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> -k | --kmer <int> identity to filter plasmids from the database with kmer approach (0-1), default 0.95</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> Contig local alignment</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -i | --alignment-identity <int> minimun identity percentage aligned for a contig to annotate, default 90</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -l | --alignment-percentage <int> minimun length percentage aligned for a contig to annotate, default 20</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -L | --length-total <int> minimun alignment length to filter blast analysis</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -i | --alignment-identity <int> minimum identity percentage aligned for a contig to annotate, default 90</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -l | --alignment-percentage <int> minimum length percentage aligned for a contig to annotate, default 20</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -L | --length-total <int> minimum alignment length to filter blast analysis</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> --extend-annotation <int> look for annotation over regions with no homology found (base pairs), default 500bp</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> Draw images:</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="p">@@ -175,7 +175,7 @@</span> Since v1.6, the more relevant output is</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> - length: length of the reference sequence</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> - species: species of the reference sequence</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> - description: rest of reference fasta header</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- - contig_name: number of the contigs that align the minimun required for complete contig track</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ - contig_name: number of the contigs that align the minimum required for complete contig track</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> - SAMPLE:</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> - Image of the reconstructed plasmid (click to open in new tab)</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> - MAPPING % (percentage): percentage of reference covered with reads</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/plasmidID</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/plasmidID</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="p">@@ -58,15 +58,15 @@</span> usage : $0 <-1 R1> <-2 R2> <-d database(</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> --no-trim Reads supplied will not be quality trimmed</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> Coverage and Clustering:</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -C | --coverage-cutoff <int> minimun coverage percentage to select a plasmid as scafold (0-100), default 80</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -S | --coverage-summary <int> minimun coverage percentage to include plasmids in summary image (0-100), default 90</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;">+ -C | --coverage-cutoff <int> minimum coverage percentage to select a plasmid as scafold (0-100), default 80</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;">+ -S | --coverage-summary <int> minimum coverage percentage to include plasmids in summary image (0-100), default 90</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> -f | --cluster <int> kmer identity to cluster plasmids into the same representative sequence (0 means identical) (0-1), default 0.5</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> -k | --kmer <int> identity to filter plasmids from the database with kmer approach (0-1), default 0.95</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> Contig local alignment</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -i | --alignment-identity <int> minimun identity percentage aligned for a contig to annotate, default 90</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -l | --alignment-percentage <int> minimun length percentage aligned for a contig to annotate, default 20</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- -L | --length-total <int> minimun alignment length to filter blast analysis</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;">+ -i | --alignment-identity <int> minimum identity percentage aligned for a contig to annotate, default 90</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ -l | --alignment-percentage <int> minimum length percentage aligned for a contig to annotate, default 20</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;">+ -L | --length-total <int> minimum alignment length to filter blast analysis</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> --extend-annotation <int> look for annotation over regions with no homology found (base pairs), default 500bp</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> Draw images:</span></pre>
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