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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/resfinder">Debian Med / resfinder</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/resfinder/commit/0a51edaf01af6a75f0b1210baeb5753548c4cd23">0a51edaf</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-06-25T13:46:49+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Initial packaging

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/resfinder/commit/86815e3ed1672c6d4b8b77e8b68793f5b2207b74">86815e3e</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-06-25T13:47:02+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.3.0</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/resfinder/commit/1e627cc718aa572f64d7adec79af8d6c11a18102">1e627cc7</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-06-25T13:47:04+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/2.3.0'

Update to upstream version '2.3.0'

with Debian dir dbaa902f3189d217c9081c4026fc306000983858</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/resfinder/commit/d8a48b9aff6740494c8f04cfb68a568148d7c06a">d8a48b9a</a></strong>

<div>

<span>by Andreas Tille</span>

<i>at 2018-06-25T15:48:29+02:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Several fixes

</pre>

</li>

</ul>

<h4>11 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

<span class="new-file">

+

debian/changelog

</span>

</a>

</li>

<li class="file-stats">

<a href="#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<span class="new-file">

+

debian/compat

</span>

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<span class="new-file">

+

debian/control

</span>

</a>

</li>

<li class="file-stats">

<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<span class="new-file">

+

debian/copyright

</span>

</a>

</li>

<li class="file-stats">

<a href="#68d8c5c6babbf5cf109b2584c454449dbff75772">

<span class="new-file">

+

debian/install

</span>

</a>

</li>

<li class="file-stats">

<a href="#efc7fe57b5983b0283c6410fceef7e74f687aeb5">

<span class="new-file">

+

debian/lintian-overrides

</span>

</a>

</li>

<li class="file-stats">

<a href="#8756c63497c8dc39f7773438edf53b220c773f67">

<span class="new-file">

+

debian/rules

</span>

</a>

</li>

<li class="file-stats">

<a href="#53399f7f2dd7535c43cdcfa511a9c06044a9c238">

<span class="new-file">

+

debian/source/format

</span>

</a>

</li>

<li class="file-stats">

<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">

<span class="new-file">

+

debian/upstream/metadata

</span>

</a>

</li>

<li class="file-stats">

<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<span class="new-file">

+

debian/watch

</span>

</a>

</li>

<li class="file-stats">

<a href="#f528b86ea4fbbf9b164847c09565a05eea2513cc">

resfinder.pl

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">resfinder (2.3.0-1) UNRELEASED; urgency=medium</span>

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="2" 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">

2

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

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Initial release (Closes: #<bug>)</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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4

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

</pre>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org>  Thu, 07 Jun 2018 21:55:00 +0200</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#78fd675df1cf8c2d4c62ae1a9a912d15c8c50ba4"><strong>debian/compat</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">11</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

<hr>

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1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Source: resfinder</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org></span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Uploaders: Andreas Tille <tille@debian.org></span>

</pre>

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<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">

4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Section: science</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Priority: optional</span>

</pre>

</td>

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6

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Build-Depends: debhelper (>= 11~)</span>

</pre>

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7

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Standards-Version: 4.1.4</span>

</pre>

</td>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/resfinder</span>

</pre>

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9

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/resfinder.git</span>

</pre>

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10

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Homepage: https://bitbucket.org/genomicepidemiology/resfinder</span>

</pre>

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11

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

</pre>

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12

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Package: resfinder</span>

</pre>

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13

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Architecture: any</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="14" 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">

14

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">Depends: ${perl:Depends},</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="15" 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">

15

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">         ${python:Depends},</span>

</pre>

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16

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">         ${misc:Depends},</span>

</pre>

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17

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

</pre>

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18

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">         ncbi-blast+-legacy</span>

</pre>

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19

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Description: identifies acquired antimicrobial resistance genes</span>

</pre>

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20

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> ResFinder identifies acquired antimicrobial resistance genes in total or</span>

</pre>

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21

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> partial sequenced isolates of bacteria.</span>

</pre>

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22

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> .</span>

</pre>

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23

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> ResFinder that uses BLAST for identification of acquired antimicrobial</span>

</pre>

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24

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> resistance genes in whole-genome data. As input, the method can use both</span>

</pre>

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25

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> pre-assembled, complete or partial genomes, and short sequence reads</span>

</pre>

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26

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> from four different sequencing platforms. The method was evaluated on</span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> 1862 GenBank files containing 1411 different resistance genes, as well</span>

</pre>

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28

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> as on 23 de-novo-sequenced isolates.</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>

<hr>

<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">

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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">

1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="2" 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">

2

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="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">

3

</td>

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Source: https://bitbucket.org/genomicepidemiology/resfinder.git</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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">

4

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="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

</td>

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Files: *</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="6" 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">

6

</td>

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Copyright: 2012-2018 Ole Lund, Technical University of Denmark </span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="7" 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">

7

</td>

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

<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">License: Apache-2.0</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="8" 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">

8

</td>

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

<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="9" 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">

9

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

10

</td>

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

<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">Copyright: 2018 Andreas Tille <tille@debian.org></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="11" 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">

11

</td>

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

<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">License: Apache-2.0</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="12" 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">

12

</td>

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

<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="13" 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">

13

</td>

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

<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">License: Apache-2.0</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="14" 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">

14

</td>

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

<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> Licensed under the Apache License, Version 2.0 (the "License");</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="15" 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">

15

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> you may not use this file except in compliance with the License.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="16" 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">

16

</td>

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

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

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> Unless required by applicable law or agreed to in writing, software</span>

</pre>

</td>

</tr>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> distributed under the License is distributed on an "AS IS" BASIS,</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">

<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="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

</td>

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

<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> See the License for the specific language governing permissions and</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="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

</td>

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

<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> limitations under the License.</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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="22" 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">

22

</td>

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

<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> .</span>

</pre>

</td>

</tr>

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

<td class="diff-line-num new old_line" data-linenumber="0" 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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23

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

<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> On Debian systems you can find the full text of the Apache-2.0</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="24" 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">

24

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

<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> license at /usr/share/common-licenses/Apache-2.0.</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="68d8c5c6babbf5cf109b2584c454449dbff75772">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#68d8c5c6babbf5cf109b2584c454449dbff75772"><strong>debian/install</strong></a>

<hr>

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</td>

<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">

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">*_DB  /usr/bin</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">*.pl  /usr/bin</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="efc7fe57b5983b0283c6410fceef7e74f687aeb5">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#efc7fe57b5983b0283c6410fceef7e74f687aeb5"><strong>debian/lintian-overrides</strong></a>

<hr>

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</td>

<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">

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># see discussion on Debian Med mailing list</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">#   https://lists.debian.org/debian-med/2018/06/msg00042.html</span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"># and following mails in thread</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">resfinder: script-with-language-extension usr/bin/resfinder.pl</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="8756c63497c8dc39f7773438edf53b220c773f67">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>

<hr>

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</td>

<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">

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">#!/usr/bin/make -f</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="2" 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">

2

</td>

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

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

</pre>

</td>

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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">

3

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

<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">%:</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">      dh $@</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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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5

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

<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="6" 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">

6

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

<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">override_dh_auto_build:</span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="0" 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="7" 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">

7

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

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

</pre>

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8

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">      echo "Upstream install target just fetches BioPerl which is now installed via Depends"</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="53399f7f2dd7535c43cdcfa511a9c06044a9c238">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#53399f7f2dd7535c43cdcfa511a9c06044a9c238"><strong>debian/source/format</strong></a>

<hr>

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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">

1

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

<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">3.0 (quilt)</span></pre>

</td>

</tr>

</table>

<br>

</li>

<li id="f5606a935d95a2f20059a7ac1136f47b2edadbf6">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>

<hr>

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</td>

<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">

1

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

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

</pre>

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2

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">  Author: Ea Zankari and Henrik Hasman and Salvatore Cosentino and Martin Vestergaard and Simon Rasmussen and Ole Lund and Frank M. Aarestrup and Mette Voldby Larsen </span>

</pre>

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3

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  Title: Identification of acquired antimicrobial resistance genes</span>

</pre>

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4

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  Journal: Journal of Antimicrobial Chemotherapy</span>

</pre>

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5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  Year: 2012</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">  Volume: 67</span>

</pre>

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7

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">  Number: 11</span>

</pre>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">  Pages: 2640-4</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">  DOI: 10.1093/jac/dks261</span>

</pre>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">  PMID: 22782487</span>

</pre>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">  URL: https://academic.oup.com/jac/article/67/11/2640/707208</span>

</pre>

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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">  eprint: https://academic.oup.com/jac/article-pdf/67/11/2640/2085909/dks261.pdf</span></pre>

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<br>

</li>

<li id="68ef9f98c01c7eecd4c605cc26048a06f3304b79">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>

<hr>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">version=4</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">https://bitbucket.org/genomicepidemiology/resfinder/downloads/?tab=tags .*/@ANY_VERSION@@ARCHIVE_EXT@</span>

</pre>

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4

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

</pre>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">#opts="mode=git,pretty=2.1+git%cd.%h" \</span>

</pre>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">#    https://bitbucket.org/genomicepidemiology/resfinder.git HEAD</span>

</pre>

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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"># In branches is totally different code ov not yet released Python code version 4.x</span>

</pre>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"># https://bitbucket.org/genomicepidemiology/resfinder/downloads/?tab=branches .*/@ANY_VERSION@@ARCHIVE_EXT@</span></pre>

</td>

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</table>

<br>

</li>

<li id="f528b86ea4fbbf9b164847c09565a05eea2513cc">

<a href="https://salsa.debian.org/med-team/resfinder/compare/4d2478f1eef0e2d0785d058d9605da45e1eef127...d8a48b9aff6740494c8f04cfb68a568148d7c06a#f528b86ea4fbbf9b164847c09565a05eea2513cc"><strong>resfinder.pl</strong></a>

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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ use Try::Tiny::Retry;</td>

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<pre style="margin: 0;"> <span id="LC10" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">constant</span> <span class="nv" style="color: teal;">PROGRAM_NAME</span>            <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'ResFinder_v2.pl'</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">constant</span> <span class="nv" style="color: teal;">PROGRAM_NAME_LONG</span>       <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'Findes antimicrobial resitance genes for a sequence or genome'</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">constant</span> <span class="nv" style="color: teal;">VERSION</span>                 <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'2.<span class="idiff left right">1</span>'</span><span class="p">;</span></span>

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: teal;">constant</span> <span class="nv" style="color: teal;">VERSION</span>                 <span class="o" style="font-weight: 600;">=></span> <span class="s" style="color: #d14;">'2.<span class="idiff left right">3</span>'</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC14" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;">#Global variables</span></span>

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$BLAST</span><span class="p">;</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">@@ -465,7 +465,7 @@ foreach my $element(@Antimicrobial){</td>

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<pre style="margin: 0;"> <span id="LC465" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$Seqs_genome_ref</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">grep_ids</span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">seqs</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: teal;">$Seqs_input</span><span class="p">,</span> <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: teal;">ids</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: teal;">@array_for_getting_genome_seq</span><span class="p">);</span>  </span>

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<pre style="margin: 0;"> <span id="LC466" class="line" lang="perl">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="nv" style="color: teal;">@</span><span class="p">{</span> <span class="nv" style="color: teal;">$Seqs_genome_ref</span> <span class="p">})</span> <span class="p">{</span></span>

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<pre style="margin: 0;"> <span id="LC467" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">lc</span><span class="p">(</span><span class="nv" style="color: teal;">$_</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: teal;">seq</span><span class="p">);</span></span>

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<pre style="margin: 0;">-<span id="LC468" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$length_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$contig</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">#Redundant, da jeg ogs<span class="idiff left right"></span> v.h.a. bioperl finder hit length</span></span>

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<pre style="margin: 0;">+<span id="LC468" class="line" lang="perl">          <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$length_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">length</span><span class="p">(</span><span class="nv" style="color: teal;">$contig</span><span class="p">);</span>  <span class="c1" style="color: #998; font-style: italic;">#Redundant, da jeg ogs<span class="idiff left right">� v</span>.h.a. bioperl finder hit length</span></span>

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<pre style="margin: 0;"> <span id="LC469" class="line" lang="perl">          </span>

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<pre style="margin: 0;"> <span id="LC470" class="line" lang="perl">          <span class="c1" style="color: #998; font-style: italic;"># Getting the right sub_contig depends on which strand the hit is on</span></span>

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<pre style="margin: 0;"> <span id="LC471" class="line" lang="perl">          <span class="c1" style="color: #998; font-style: italic;"># If the hit is on the +1 </span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="490" 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="490" 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">@@ -490,7 +490,7 @@ foreach my $element(@Antimicrobial){</td>

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<pre style="margin: 0;"> <span id="LC490" class="line" lang="perl">                <span class="nv" style="color: teal;">$variant</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC491" class="line" lang="perl">                <span class="nv" style="color: teal;">$major_variants_detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC492" class="line" lang="perl">                <span class="nv" style="color: teal;">$sub_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: teal;">$contig</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span>  <span class="p">(</span> <span class="nv" style="color: teal;">$HIT_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="nv" style="color: teal;">$QUERY_LENGTH</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: teal;">$no_gaps_gene</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">})));</span></span>

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<pre style="margin: 0;">-<span id="LC493" class="line" lang="perl">                <span class="c1" style="color: #998; font-style: italic;">#If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||<span class="idiff left right">Ê|||Ê</span>||") should be preceeded by spaces</span></span>

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<pre style="margin: 0;">+<span id="LC493" class="line" lang="perl">                <span class="c1" style="color: #998; font-style: italic;">#If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||<span class="idiff left right">�|||�||")</span> should be preceeded by spaces</span></span>

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<pre style="margin: 0;"> <span id="LC494" class="line" lang="perl">                <span class="nv" style="color: teal;">$spaces_hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$HIT_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC495" class="line" lang="perl">                <span class="nv" style="color: teal;">$spaces_match_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC496" class="line" lang="perl">              <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span>    </span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="705" 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">@@ -705,7 +705,7 @@ foreach my $element(@Antimicrobial){</td>

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<pre style="margin: 0;"> <span id="LC705" class="line" lang="perl">                <span class="nv" style="color: teal;">$variant</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">4</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC706" class="line" lang="perl">                <span class="nv" style="color: teal;">$major_variants_detector</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC707" class="line" lang="perl">                <span class="nv" style="color: teal;">$sub_contig</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">substr</span><span class="p">(</span><span class="nv" style="color: teal;">$contig</span><span class="p">,</span> <span class="mi" style="color: #099;">0</span><span class="p">,</span>  <span class="p">(</span> <span class="nv" style="color: teal;">$HIT_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="p">((</span><span class="nv" style="color: teal;">$QUERY_LENGTH</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="nv" style="color: teal;">$no_gaps_gene</span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">})));</span></span>

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<pre style="margin: 0;">-<span id="LC708" class="line" lang="perl">                <span class="c1" style="color: #998; font-style: italic;"># If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||<span class="idiff left right">Ê|||Ê</span>||") should be preceeded by spaces</span></span>

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<pre style="margin: 0;">+<span id="LC708" class="line" lang="perl">                <span class="c1" style="color: #998; font-style: italic;"># If, as here, the HSP only starts some nucleotides within the mlst allele, a number of spaces must be written before the matching string from the genome. Likewise, the match-string (the "||<span class="idiff left right">�|||�||")</span> should be preceeded by spaces</span></span>

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<pre style="margin: 0;"> <span id="LC709" class="line" lang="perl">                <span class="nv" style="color: teal;">$spaces_hit</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">-</span> <span class="nv" style="color: teal;">$HIT_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">}</span> <span class="o" style="font-weight: 600;">+</span> <span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="710" 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="LC710" class="line" lang="perl">                <span class="nv" style="color: teal;">$spaces_match_string</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$QUERY_START</span><span class="p">{</span><span class="nv" style="color: teal;">$data</span><span class="p">};</span></span>

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<pre style="margin: 0;"> <span id="LC711" class="line" lang="perl">              <span class="p">}</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="860" 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="860" 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">@@ -860,7 +860,7 @@ foreach my $element(@Antimicrobial){</td>

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<pre style="margin: 0;"> <span id="LC860" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;">#print $ABres_substr . "\n";</span></span>

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<td class="diff-line-num old_line" data-linenumber="861" 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="LC861" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">push</span><span class="p">(</span><span class="nv" style="color: teal;">@</span><span class="p">{</span><span class="nv" style="color: teal;">$GENE_ALIGN_QUERY_HASH</span><span class="p">{</span><span class="nv" style="color: teal;">$gene</span><span class="p">}},</span> <span class="nv" style="color: teal;">$ABres_substr</span><span class="p">);</span></span>

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<td class="diff-line-num old_line" data-linenumber="862" 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="LC862" class="line" lang="perl">   </span>

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<td class="diff-line-num old old_line" data-linenumber="863" 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="LC863" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;">#Printing spaces before the match string with the "||<span class="idiff left right">Ê||||Ê||Ê</span>||" and the string itself</span></span>

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<pre style="margin: 0;">+<span id="LC863" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;">#Printing spaces before the match string with the "||<span class="idiff left right">�||||�||�||" an</span>d the string itself</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC864" class="line" lang="perl">        <span class="c1" style="color: #998; font-style: italic;">#print "                   ";</span></span>

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<td class="diff-line-num old_line" data-linenumber="865" 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="LC865" class="line" lang="perl">        <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$string_spaces</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">""</span><span class="p">;</span>  <span class="c1" style="color: #998; font-style: italic;">#For saving the spaces as a string of spaces instead of a number of spaces</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC866" class="line" lang="perl">        <span class="k" style="font-weight: 600;">for</span> <span class="p">(</span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">1</span> <span class="p">;</span> <span class="nv" style="color: teal;">$i</span> <span class="o" style="font-weight: 600;"><</span> <span class="nv" style="color: teal;">$spaces_match_string</span><span class="p">;</span> <span class="o" style="font-weight: 600;">++</span><span class="nv" style="color: teal;">$i</span><span class="p">){</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="969" 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="969" 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">@@ -969,7 +969,7 @@ foreach my $key (sort keys %GENE_RESULTS_HASH2) {</td>

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<pre style="margin: 0;"> <span id="LC969" class="line" lang="perl">    <span class="nv" style="color: teal;">$outStr</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: teal;">$outStr</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">": WARNING2, "</span><span class="p">;</span> </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="970" 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="LC970" class="line" lang="perl">  <span class="p">}</span>  </span>

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<pre style="margin: 0;"> <span id="LC971" class="line" lang="perl">  <span class="nv" style="color: teal;">$alignment</span> <span class="o" style="font-weight: 600;">.=</span> <span class="nv" style="color: teal;">$outStr</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"ID: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"%, HSP/Length: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">", Contig name: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Position: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n\n"</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC972" class="line" lang="perl">  <span class="nv" style="color: teal;">$hits_in_seq</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$outStr</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"ID: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"%, HSP/Length: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">", Positions in reference: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qStart</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">".."</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qEnd</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Contig name: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Position: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#m<span class="idiff left right"></span>ske forkert text</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="973" 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="972" 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">

972

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<pre style="margin: 0;">+<span id="LC972" class="line" lang="perl">  <span class="nv" style="color: teal;">$hits_in_seq</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$outStr</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"ID: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">1</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"%, HSP/Length: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">3</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"/"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">2</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span> <span class="s" style="color: #d14;">", Positions in reference: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qStart</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">".."</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">$qEnd</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Contig name: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">4</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">", Position: "</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">5</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="p">;</span> <span class="c1" style="color: #998; font-style: italic;">#m<span class="idiff left right">�sk</span>e forkert text</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="973" 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">

973

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<td class="diff-line-num new_line" data-linenumber="973" 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">

973

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<pre style="margin: 0;"> <span id="LC973" class="line" lang="perl">  <span class="nv" style="color: teal;">$resalign</span> <span class="o" style="font-weight: 600;">.=</span> <span class="s" style="color: #d14;">">"</span><span class="o" style="font-weight: 600;">.</span><span class="nv" style="color: teal;">@$array</span><span class="p">[</span><span class="mi" style="color: #099;">7</span><span class="p">]</span><span class="o" style="font-weight: 600;">.</span><span class="s" style="color: #d14;">"\n"</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="974" 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">

974

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<td class="diff-line-num new_line" data-linenumber="974" 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">

974

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

<pre style="margin: 0;"> <span id="LC974" class="line" lang="perl">  </span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="975" 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">

975

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<td class="diff-line-num new_line" data-linenumber="975" 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">

975

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

<pre style="margin: 0;"> <span id="LC975" class="line" lang="perl">  <span class="c1" style="color: #998; font-style: italic;"># now print the alleles</span></span>

</pre>

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