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GitLab

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<h3>

Michael R. Crusoe pushed to branch upstream

at <a href="https://salsa.debian.org/med-team/libbio-variation-perl">Debian Med / libbio-variation-perl</a>

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0">95dd8455</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2020-01-07T14:23:58+01:00</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 1.7.5</pre>

</li>

</ul>

<h4>21 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#8aa57de6dce6ee1c35c6aba7426503281876b258">

Changes

</a>

</li>

<li class="file-stats">

<a href="#0398ccd0f49298b10a3d76a47800d2ebecd49859">

LICENSE

</a>

</li>

<li class="file-stats">

<a href="#9ae61f13c66eb261147f9d4b1d89a27b5c697890">

MANIFEST

</a>

</li>

<li class="file-stats">

<a href="#4a6da301633ce81aa21cac64ffb95d87c6894995">

META.json

</a>

</li>

<li class="file-stats">

<a href="#3b7f8f92275828b66b32cb6c6aeb61e73c1d7587">

META.yml

</a>

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<li class="file-stats">

<a href="#a6a4139b0f32af1594c237ebe008acaf8217f505">

Makefile.PL

</a>

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<li class="file-stats">

<a href="#416465dfe053b24978813c7c1c215330be966d3e">

bin/bp_flanks

</a>

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<li class="file-stats">

<a href="#384adeead2ae33537082bc3db4b10a27220e76ca">

dist.ini

</a>

</li>

<li class="file-stats">

<a href="#860c894f76026ba2f4228857a6ec3699da75dbc9">

lib/Bio/Variation.pm

</a>

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<li class="file-stats">

<a href="#a17d804eb208f51efc62cedddba0dd5fc021066b">

lib/Bio/Variation/AAChange.pm

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<li class="file-stats">

<a href="#fa1ce291cc95312c601c6ffb2b662cddcace940d">

lib/Bio/Variation/AAReverseMutate.pm

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<li class="file-stats">

<a href="#1d5e0b89f8a1dab378c4116ab66a3d16ea0c69df">

lib/Bio/Variation/Allele.pm

</a>

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<li class="file-stats">

<a href="#37c8b44f7b6a505391243b288a619d7928f06d9d">

lib/Bio/Variation/DNAMutation.pm

</a>

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<li class="file-stats">

<a href="#74ef1fa2d9266baf8d5ee894426f943aa1d70509">

lib/Bio/Variation/IO.pm

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<li class="file-stats">

<a href="#caf6f454b5383691278978fcdadeeaf8e6c533c0">

lib/Bio/Variation/IO/flat.pm

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<li class="file-stats">

<a href="#48a56f92704de7600c65a931a93e4c8900a5e0da">

lib/Bio/Variation/IO/xml.pm

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<li class="file-stats">

<a href="#a0aabaa3ef3d83b4441855fd5c86502d264a6e7b">

<span class="deleted-file">

−

lib/Bio/Variation/README

</span>

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<li class="file-stats">

<a href="#bb802b019691ae4bef7db35fce466f358f1fa284">

lib/Bio/Variation/RNAChange.pm

</a>

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<li class="file-stats">

<a href="#789d8a42ca4aba466e884536281e26fa5e9afc97">

lib/Bio/Variation/SNP.pm

</a>

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<li class="file-stats">

<a href="#0d0a9aaab5bb3ce4c26aa129ee6c529d67968a0a">

lib/Bio/Variation/SeqDiff.pm

</a>

</li>

<li class="file-stats">

<a href="#5a0af526767c1358b8a94a876e6a8263a5053e54">

lib/Bio/Variation/VariantI.pm

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="8aa57de6dce6ee1c35c6aba7426503281876b258">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#8aa57de6dce6ee1c35c6aba7426503281876b258"><strong>Changes</strong></a>

<hr>

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1

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1

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Summary of important user-visible changes for Bio-Variation</span>

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2

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

</pre>

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3

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3

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

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">1.7.5     2020-01-06 13:58:44-06:00 America/Chicago</span>

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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">

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * Remove Bio::DB::EMBL and Bio::DB::NCBIHelper dependencies, which cause a circular dependency (see issue #3)</span>

</pre>

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6

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

</pre>

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4

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">1.7.4     2019-12-07 16:56:21-06:00 America/Chicago</span>

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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">  * Add named module (very simple for now)</span>

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">  * Minor release to address CPAN indexing and permissions issues</span>

</pre>

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<br>

</li>

<li id="0398ccd0f49298b10a3d76a47800d2ebecd49859">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#0398ccd0f49298b10a3d76a47800d2ebecd49859"><strong>LICENSE</strong></a>

<hr>

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

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1

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

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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">This software is copyright (c) 20<span class="idiff left right">19</span> by See individual modules.</span>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">This software is copyright (c) 20<span class="idiff left right">20</span> by See individual modules.</span>

</pre>

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">This is free software; you can redistribute it and/or modify it under</span>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">the same terms as the Perl 5 programming language system itself.</span>

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<td class="diff-line-num unfold js-unfold 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">...</td>

<td class="diff-line-num unfold js-unfold new_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">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -12,7 +12,7 @@ b) the "Artistic License"</td>

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

</pre>

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<td class="diff-line-num new_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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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext">--- The GNU General Public License, Version 1, February 1989 ---</span>

</pre>

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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">

14

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext">This software is Copyright (c) 20<span class="idiff left right">19</span> by See individual modules.</span>

</pre>

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<td class="diff-line-num new old_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">

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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">

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

<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">This software is Copyright (c) 20<span class="idiff left right">20</span> by See individual modules.</span>

</pre>

</td>

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

16

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

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

</pre>

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<td class="diff-line-num old_line" data-linenumber="17" 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="17" 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="LC17" class="line" lang="plaintext">This is free software, licensed under:</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="18" 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="18" 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="LC18" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="272" 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="272" 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">@@ -272,7 +272,7 @@ That's all there is to it!</td>

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<td class="diff-line-num old_line" data-linenumber="272" 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="272" 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="LC272" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="273" 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="273" 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="LC273" class="line" lang="plaintext">--- The Artistic License 1.0 ---</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="274" 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="274" 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="LC274" class="line" lang="plaintext"></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="275" 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="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC275" class="line" lang="plaintext">This software is Copyright (c) 20<span class="idiff left right">19</span> by See individual modules.</span>

</pre>

</td>

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<td class="diff-line-num new old_line" data-linenumber="276" 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="275" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

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

<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">This software is Copyright (c) 20<span class="idiff left right">20</span> by See individual modules.</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="276" 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="276" 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="LC276" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="277" 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="277" 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="LC277" class="line" lang="plaintext">This is free software, licensed under:</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="278" 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="278" 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="LC278" class="line" lang="plaintext"></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="9ae61f13c66eb261147f9d4b1d89a27b5c697890">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#9ae61f13c66eb261147f9d4b1d89a27b5c697890"><strong>MANIFEST</strong></a>

<hr>

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

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -15,7 +15,6 @@ lib/Bio/Variation/DNAMutation.pm</td>

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

15

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

15

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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">lib/Bio/Variation/IO.pm</span>

</pre>

</td>

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

16

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

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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">lib/Bio/Variation/IO/flat.pm</span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="17" 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">

17

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<td class="diff-line-num new_line" data-linenumber="17" 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="LC17" class="line" lang="plaintext">lib/Bio/Variation/IO/xml.pm</span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext">lib/Bio/Variation/README</span>

</pre>

</td>

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19

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

18

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">lib/Bio/Variation/RNAChange.pm</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line" data-linenumber="19" 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">

19

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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">lib/Bio/Variation/SNP.pm</span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" 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">

21

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<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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

<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext">lib/Bio/Variation/SeqDiff.pm</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="4a6da301633ce81aa21cac64ffb95d87c6894995">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#4a6da301633ce81aa21cac64ffb95d87c6894995"><strong>META.json</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="diff-line-num unfold js-unfold new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -30,8 +30,6 @@</td>

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<td class="diff-line-num new_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="json"><span class="w" style="color: #bbb;">      </span><span class="p">},</span></span>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="json"><span class="w" style="color: #bbb;">      </span><span class="nl">"runtime"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="32" 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="32" 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="LC32" class="line" lang="json"><span class="w" style="color: #bbb;">         </span><span class="nl">"requires"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="33" 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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC33" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"Bio::DB::EMBL"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="34" 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="33" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC34" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"Bio::DB::GenBank"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="35" 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">

35

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<td class="diff-line-num new_line" data-linenumber="33" 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="LC33" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"Bio::DBLinkContainerI"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="36" 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="34" 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="LC34" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"Bio::PrimarySeq"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="37" 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="35" 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="LC35" class="line" lang="json"><span class="w" style="color: #bbb;">            </span><span class="nl">"Bio::Root::IO"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"0"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="77" 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="75" 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">@@ -77,7 +75,7 @@</td>

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<pre style="margin: 0;"> <span id="LC75" class="line" lang="json"><span class="w" style="color: #bbb;">         </span><span class="nl">"web"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"https://github.com/bioperl/bio-variation"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="78" 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="76" 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="LC76" class="line" lang="json"><span class="w" style="color: #bbb;">      </span><span class="p">}</span></span>

</pre>

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<td class="diff-line-num new_line" data-linenumber="77" 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="LC77" class="line" lang="json"><span class="w" style="color: #bbb;">   </span><span class="p">},</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="80" 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="78" 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="LC80" class="line" lang="json"><span class="w" style="color: #bbb;">   </span><span class="nl">"version"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1.7.<span class="idiff left right">4</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="81" 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="78" 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="LC78" class="line" lang="json"><span class="w" style="color: #bbb;">   </span><span class="nl">"version"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"1.7.<span class="idiff left right">5</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="81" 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="79" 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="LC79" class="line" lang="json"><span class="w" style="color: #bbb;">   </span><span class="nl">"x_Dist_Zilla"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="82" 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="LC80" class="line" lang="json"><span class="w" style="color: #bbb;">      </span><span class="nl">"perl"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="83" 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="81" 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="LC81" class="line" lang="json"><span class="w" style="color: #bbb;">         </span><span class="nl">"version"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"5.028001"</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="297" 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="295" 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">@@ -297,7 +295,7 @@</td>

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<td class="diff-line-num old_line" data-linenumber="297" 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="295" 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="LC295" class="line" lang="json"><span class="w" style="color: #bbb;">                  </span><span class="nl">"branch"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">null</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="298" 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="296" 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="LC296" class="line" lang="json"><span class="w" style="color: #bbb;">                  </span><span class="nl">"changelog"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Changes"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="299" 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="297" 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="LC297" class="line" lang="json"><span class="w" style="color: #bbb;">                  </span><span class="nl">"signed"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="mi" style="color: #099;">0</span><span class="p">,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="300" 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="298" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC300" class="line" lang="json"><span class="w" style="color: #bbb;">                  </span><span class="nl">"tag"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Bio-Variation-v1.7.<span class="idiff left right">4</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="301" 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="298" 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="LC298" class="line" lang="json"><span class="w" style="color: #bbb;">                  </span><span class="nl">"tag"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"Bio-Variation-v1.7.<span class="idiff left right">5</span>"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="301" 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="299" 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="LC299" class="line" lang="json"><span class="w" style="color: #bbb;">                  </span><span class="nl">"tag_format"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"%N-v%v"</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="302" 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="300" 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="LC300" class="line" lang="json"><span class="w" style="color: #bbb;">                  </span><span class="nl">"tag_message"</span><span class="w" style="color: #bbb;"> </span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"%N-v%v"</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="303" 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="301" 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="LC301" class="line" lang="json"><span class="w" style="color: #bbb;">               </span><span class="p">},</span></span>

</pre>

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<br>

</li>

<li id="3b7f8f92275828b66b32cb6c6aeb61e73c1d7587">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#3b7f8f92275828b66b32cb6c6aeb61e73c1d7587"><strong>META.yml</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" 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="21" 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">@@ -21,8 +21,6 @@ meta-spec:</td>

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<td class="diff-line-num old_line" data-linenumber="21" 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="21" 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="LC21" class="line" lang="yaml">  <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">1.4'</span></span>

</pre>

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

22

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<td class="diff-line-num new_line" data-linenumber="22" 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">

22

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<pre style="margin: 0;"> <span id="LC22" class="line" lang="yaml"><span class="na" style="color: #008080;">name</span><span class="pi">:</span> <span class="s" style="color: #d14;">Bio-Variation</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="23" 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="23" 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="LC23" class="line" lang="yaml"><span class="na" style="color: #008080;">requires</span><span class="pi">:</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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="24" 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="LC24" class="line" lang="yaml">  <span class="s" style="color: #d14;">Bio::DB::EMBL: '0'</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line old" data-linenumber="24" 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="LC25" class="line" lang="yaml">  <span class="s" style="color: #d14;">Bio::DB::GenBank: '0'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="26" 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="24" 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">

24

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<pre style="margin: 0;"> <span id="LC24" class="line" lang="yaml">  <span class="s" style="color: #d14;">Bio::DBLinkContainerI: '0'</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="25" 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="LC25" class="line" lang="yaml">  <span class="s" style="color: #d14;">Bio::PrimarySeq: '0'</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC26" class="line" lang="yaml">  <span class="s" style="color: #d14;">Bio::Root::IO: '0'</span></span>

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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="43" 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">@@ -45,7 +43,7 @@ resources:</td>

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<pre style="margin: 0;"> <span id="LC43" class="line" lang="yaml">  <span class="na" style="color: #008080;">bugtracker</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://github.com/bioperl/bio-variation/issues</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC44" class="line" lang="yaml">  <span class="na" style="color: #008080;">homepage</span><span class="pi">:</span> <span class="s" style="color: #d14;">https://metacpan.org/release/Bio-Variation</span></span>

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<pre style="margin: 0;"> <span id="LC45" class="line" lang="yaml">  <span class="na" style="color: #008080;">repository</span><span class="pi">:</span> <span class="s" style="color: #d14;">git://github.com/bioperl/bio-variation.git</span></span>

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<pre style="margin: 0;">-<span id="LC48" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s" style="color: #d14;">1.7.<span class="idiff left right">4</span></span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="yaml"><span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s" style="color: #d14;">1.7.<span class="idiff left right">5</span></span></span>

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<pre style="margin: 0;"> <span id="LC47" class="line" lang="yaml"><span class="na" style="color: #008080;">x_Dist_Zilla</span><span class="pi">:</span></span>

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<pre style="margin: 0;"> <span id="LC48" class="line" lang="yaml">  <span class="na" style="color: #008080;">perl</span><span class="pi">:</span></span>

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="yaml">    <span class="na" style="color: #008080;">version</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">5.028001'</span></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="218" 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="216" 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">@@ -218,7 +216,7 @@ x_Dist_Zilla:</td>

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<pre style="margin: 0;"> <span id="LC216" class="line" lang="yaml">          <span class="s" style="color: #d14;">branch</span><span class="pi">:</span> <span class="s" style="color: #d14;">~</span></span>

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<pre style="margin: 0;"> <span id="LC217" class="line" lang="yaml">          <span class="s" style="color: #d14;">changelog</span><span class="pi">:</span> <span class="s" style="color: #d14;">Changes</span></span>

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<pre style="margin: 0;"> <span id="LC218" class="line" lang="yaml">          <span class="s" style="color: #d14;">signed</span><span class="pi">:</span> <span class="m" style="color: #099;">0</span></span>

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<pre style="margin: 0;">-<span id="LC221" class="line" lang="yaml">          <span class="na" style="color: #008080;">tag</span><span class="pi">:</span> <span class="s" style="color: #d14;">Bio-Variation-v1.7.<span class="idiff left right">4</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="222" 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="LC219" class="line" lang="yaml">          <span class="na" style="color: #008080;">tag</span><span class="pi">:</span> <span class="s" style="color: #d14;">Bio-Variation-v1.7.<span class="idiff left right">5</span></span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC220" class="line" lang="yaml">          <span class="na" style="color: #008080;">tag_format</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">%N-v%v'</span></span>

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<pre style="margin: 0;"> <span id="LC221" class="line" lang="yaml">          <span class="na" style="color: #008080;">tag_message</span><span class="pi">:</span> <span class="s1" style="color: #d14;">'</span><span class="s" style="color: #d14;">%N-v%v'</span></span>

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<pre style="margin: 0;"> <span id="LC222" class="line" lang="yaml">        <span class="s" style="color: #d14;">Dist::Zilla::Role::Git::Repo:</span></span>

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<br>

</li>

<li id="a6a4139b0f32af1594c237ebe008acaf8217f505">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#a6a4139b0f32af1594c237ebe008acaf8217f505"><strong>Makefile.PL</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="20" 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="20" 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">@@ -20,8 +20,6 @@ my %WriteMakefileArgs = (</td>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

20

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<td class="diff-line-num new_line" data-linenumber="20" 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">

20

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<pre style="margin: 0;"> <span id="LC20" class="line" lang="make">  <span class="s2" style="color: #d14;">"MIN_PERL_VERSION"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;">"5.006"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="21" 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">

21

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<td class="diff-line-num new_line" data-linenumber="21" 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">

21

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<pre style="margin: 0;"> <span id="LC21" class="line" lang="make">  <span class="s2" style="color: #d14;">"NAME"</span> <span class="nl">=> "Bio</span><span class="o" style="font-weight: 600;">::</span><span class="nf" style="color: #900; font-weight: 600;">Variation"</span><span class="p">,</span></span>

</pre>

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

22

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<td class="diff-line-num new_line" data-linenumber="22" 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">

22

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

<pre style="margin: 0;"> <span id="LC22" class="line" lang="make">  <span class="s2" style="color: #d14;">"PREREQ_PM"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>

</pre>

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

23

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

</td>

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

<pre style="margin: 0;">-<span id="LC23" class="line" lang="make">    <span class="s2" style="color: #d14;">"Bio::DB::EMBL"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

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

</td>

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

<pre style="margin: 0;">-<span id="LC24" class="line" lang="make">    <span class="s2" style="color: #d14;">"Bio::DB::GenBank"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="25" 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">

25

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<td class="diff-line-num new_line" data-linenumber="23" 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">

23

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

<pre style="margin: 0;"> <span id="LC23" class="line" lang="make">    <span class="s2" style="color: #d14;">"Bio::DBLinkContainerI"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="26" 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">

26

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

24

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

<pre style="margin: 0;"> <span id="LC24" class="line" lang="make">    <span class="s2" style="color: #d14;">"Bio::PrimarySeq"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

27

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<td class="diff-line-num new_line" data-linenumber="25" 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">

25

</td>

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

<pre style="margin: 0;"> <span id="LC25" class="line" lang="make">    <span class="s2" style="color: #d14;">"Bio::Root::IO"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="49" 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="47" 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">@@ -49,7 +47,7 @@ my %WriteMakefileArgs = (</td>

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<td class="diff-line-num old_line" data-linenumber="49" 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">

49

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<td class="diff-line-num new_line" data-linenumber="47" 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">

47

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

<pre style="margin: 0;"> <span id="LC47" class="line" lang="make">    <span class="s2" style="color: #d14;">"Test::More"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="50" 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">

50

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<td class="diff-line-num new_line" data-linenumber="48" 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">

48

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

<pre style="margin: 0;"> <span id="LC48" class="line" lang="make">    <span class="s2" style="color: #d14;">"lib"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="51" 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">

51

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<td class="diff-line-num new_line" data-linenumber="49" 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">

49

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<pre style="margin: 0;"> <span id="LC49" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">},</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num old old_line" data-linenumber="52" 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">

52

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<td class="diff-line-num new_line old" data-linenumber="50" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC52" class="line" lang="make">  <span class="s2" style="color: #d14;">"VERSION"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;">"1.7.<span class="idiff left right">4</span>"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></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="53" 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="50" 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">

50

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

<pre style="margin: 0;">+<span id="LC50" class="line" lang="make">  <span class="s2" style="color: #d14;">"VERSION"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;">"1.7.<span class="idiff left right">5</span>"</span><span class="err" style="color: #a61717; background-color: #e3d2d2;">,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="53" 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">

53

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<td class="diff-line-num new_line" data-linenumber="51" 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">

51

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

<pre style="margin: 0;"> <span id="LC51" class="line" lang="make">  <span class="s2" style="color: #d14;">"test"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">{</span></span>

</pre>

</td>

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

<td class="diff-line-num old_line" data-linenumber="54" 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">

54

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<td class="diff-line-num new_line" data-linenumber="52" 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">

52

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

<pre style="margin: 0;"> <span id="LC52" class="line" lang="make">    <span class="s2" style="color: #d14;">"TESTS"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="s2" style="color: #d14;">"t/*.t"</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="55" 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">

55

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<td class="diff-line-num new_line" data-linenumber="53" 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">

53

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

<pre style="margin: 0;"> <span id="LC53" class="line" lang="make">  <span class="err" style="color: #a61717; background-color: #e3d2d2;">}</span></span>

</pre>

</td>

</tr>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="57" 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="55" 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">@@ -57,8 +55,6 @@ my %WriteMakefileArgs = (</td>

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<td class="diff-line-num old_line" data-linenumber="57" 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">

57

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<td class="diff-line-num new_line" data-linenumber="55" 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">

55

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

<pre style="margin: 0;"> <span id="LC55" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="58" 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">

58

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<td class="diff-line-num new_line" data-linenumber="56" 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">

56

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

<pre style="margin: 0;"> <span id="LC56" class="line" lang="make"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="59" 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">

59

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<td class="diff-line-num new_line" data-linenumber="57" 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">

57

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<pre style="margin: 0;"> <span id="LC57" class="line" lang="make"><span class="err" style="color: #a61717; background-color: #e3d2d2;">my</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">%</span><span class="nv" style="color: #008080;">FallbackPrereqs</span> <span class="o" style="font-weight: 600;">=</span> <span class="o" style="font-weight: 600;">(</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="60" 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">

60

</td>

<td class="diff-line-num new_line old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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

<pre style="margin: 0;">-<span id="LC60" class="line" lang="make">  <span class="s2" style="color: #d14;">"Bio::DB::EMBL"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="61" 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">

61

</td>

<td class="diff-line-num new_line old" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

</td>

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<pre style="margin: 0;">-<span id="LC61" class="line" lang="make">  <span class="s2" style="color: #d14;">"Bio::DB::GenBank"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" 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">

62

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<td class="diff-line-num new_line" data-linenumber="58" 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">

58

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

<pre style="margin: 0;"> <span id="LC58" class="line" lang="make">  <span class="s2" style="color: #d14;">"Bio::DBLinkContainerI"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="63" 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">

63

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<td class="diff-line-num new_line" data-linenumber="59" 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">

59

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

<pre style="margin: 0;"> <span id="LC59" class="line" lang="make">  <span class="s2" style="color: #d14;">"Bio::PrimarySeq"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="64" 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">

64

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<td class="diff-line-num new_line" data-linenumber="60" 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">

60

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

<pre style="margin: 0;"> <span id="LC60" class="line" lang="make">  <span class="s2" style="color: #d14;">"Bio::Root::IO"</span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">=></span> <span class="err" style="color: #a61717; background-color: #e3d2d2;">0,</span></span>

</pre>

</td>

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</table>

<br>

</li>

<li id="416465dfe053b24978813c7c1c215330be966d3e">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#416465dfe053b24978813c7c1c215330be966d3e"><strong>bin/bp_flanks</strong></a>

<hr>

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

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -14,8 +14,6 @@</td>

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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">

14

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

14

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

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

</pre>

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

15

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

15

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

<pre style="margin: 0;"> <span id="LC15" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">PrimarySeq</span><span class="p">;</span></span>

</pre>

</td>

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

16

</td>

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

16

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

<pre style="margin: 0;"> <span id="LC16" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="p">;</span></span>

</pre>

</td>

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

17

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC17" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">EMBL</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

</td>

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

</td>

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

<pre style="margin: 0;">-<span id="LC18" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="19" 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">

19

</td>

<td class="diff-line-num new_line" data-linenumber="17" 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">

17

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<pre style="margin: 0;"> <span id="LC17" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Getopt::</span><span class="nv" style="color: #008080;">Long</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="20" 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">

20

</td>

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

18

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

<pre style="margin: 0;"> <span id="LC18" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

</td>

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<td class="diff-line-num old_line" data-linenumber="21" 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">

21

</td>

<td class="diff-line-num new_line" data-linenumber="19" 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">

19

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

<pre style="margin: 0;"> <span id="LC19" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</span><span class="p">;</span></span>

</pre>

</td>

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

<td class="diff-line-num unfold js-unfold old_line" data-linenumber="25" 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="23" 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">@@ -25,9 +23,11 @@ use constant VERSION => '3.0';</td>

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<td class="diff-line-num old_line" data-linenumber="25" 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">

25

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<pre style="margin: 0;"> <span id="LC23" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$help</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'';</span></span>

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<td class="diff-line-num old_line" data-linenumber="26" 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="24" 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="LC24" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$flank</span> <span class="o" style="font-weight: 600;">=</span> <span class="mi" style="color: #099;">100</span><span class="p">;</span>              <span class="c1" style="color: #998; font-style: italic;"># flank length on both sides of the region</span></span>

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<td class="diff-line-num new_line" data-linenumber="25" 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="LC25" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$in_format</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">EMBL</span><span class="p">';</span>       <span class="c1" style="color: #998; font-style: italic;"># format of the file to read in</span></span>

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<td class="diff-line-num new old_line" data-linenumber="28" 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="26" 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="LC26" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># my $db_class = 'Bio::DB::EMBL';  # class of</span></span>

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<td class="diff-line-num old_line" data-linenumber="28" 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="27" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC27" class="line" lang="perl"><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">@pos</span><span class="p">;</span>                      <span class="c1" style="color: #998; font-style: italic;"># position(s) in the sequence</span></span>

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<td class="diff-line-num old_line" data-linenumber="29" 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="28" 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="LC28" class="line" lang="perl"></span>

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<td class="diff-line-num old_line" data-linenumber="30" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<td class="diff-line-num new_line" data-linenumber="29" 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="LC29" class="line" lang="perl"></span>

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<td class="diff-line-num new old_line" data-linenumber="31" 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="LC30" class="line" lang="perl"></span>

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<td class="diff-line-num old_line" data-linenumber="31" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

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<pre style="margin: 0;"> <span id="LC31" class="line" lang="perl"><span class="nv" style="color: #008080;">GetOptions</span> <span class="p">("</span><span class="s2" style="color: #d14;">help</span><span class="p">"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">$help</span><span class="p">,</span> <span class="p">"</span><span class="s2" style="color: #d14;">flanklength=i</span><span class="p">"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">$flank</span><span class="p">,</span></span>

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<td class="diff-line-num old_line" data-linenumber="32" 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="32" 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="LC32" class="line" lang="perl">            <span class="p">"</span><span class="s2" style="color: #d14;">position=s</span><span class="p">"</span> <span class="o" style="font-weight: 600;">=></span> <span class="o" style="font-weight: 600;">\</span><span class="nv" style="color: #008080;">@pos</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="33" 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="33" 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="LC33" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="55" 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="55" 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">@@ -55,21 +55,28 @@ sub get_seq {</td>

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<pre style="margin: 0;"> <span id="LC55" class="line" lang="perl">    <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$IN_FORMAT</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">EMBL</span><span class="p">';</span>      <span class="c1" style="color: #998; font-style: italic;"># format of the local file on disk</span></span>

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<td class="diff-line-num old_line" data-linenumber="56" 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="56" 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="LC56" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="57" 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="57" 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="LC57" class="line" lang="perl">    <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">e</span> <span class="nv" style="color: #008080;">$file</span> <span class="p">)</span> <span class="p">{</span>             <span class="c1" style="color: #998; font-style: italic;"># local file</span></span>

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<td class="diff-line-num old old_line" data-linenumber="58" 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="58" 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="LC58" class="line" lang="perl"><span class="idiff left right">   </span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$in</span>  <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-file</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$file</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="58" 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="LC59" class="line" lang="perl"><span class="idiff left right">                           </span>  <span class="p">'</span><span class="s1" style="color: #d14;">-format</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$IN_FORMAT</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="60" 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="58" 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="LC60" class="line" lang="perl"><span class="idiff left right">   </span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$in</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">next_seq</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="61" 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="58" 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">

58

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="perl"><span class="idiff left right">        </span><span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$in</span>  <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">('</span><span class="s1" style="color: #d14;">-file</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$file</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="61" 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="59" 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">

59

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="perl"><span class="idiff left right">                    </span>  <span class="p">'</span><span class="s1" style="color: #d14;">-format</span><span class="p">'</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$IN_FORMAT</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="61" 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="60" 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="LC60" class="line" lang="perl"><span class="idiff left right">        </span><span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$in</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">next_seq</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="61" 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">

61

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<td class="diff-line-num new_line" data-linenumber="61" 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">

61

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="perl">    <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="62" 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">

62

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<td class="diff-line-num new_line" data-linenumber="62" 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="LC62" class="line" lang="perl">    <span class="k" style="font-weight: 600;">elsif</span> <span class="p">(</span><span class="nv" style="color: #008080;">$file</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">/\./</span><span class="p">)</span> <span class="p">{</span>      <span class="c1" style="color: #998; font-style: italic;"># sequence version from GenBank</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="63" 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="63" 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="LC63" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" 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="63" 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="LC64" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="65" 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="63" 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="LC65" class="line" lang="perl">      <span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_version</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="66" 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="63" 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="LC66" class="line" lang="perl">  <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="63" 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="LC63" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="64" 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="LC64" class="line" lang="perl">            <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_load_module</span><span class="p">("</span><span class="s2" style="color: #d14;">Bio::DB::GenBank</span><span class="p">");</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="65" 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="LC65" class="line" lang="perl">            <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">GenBank</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">();</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="66" 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="LC66" class="line" lang="perl">            <span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_version</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="67" 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="LC67" class="line" lang="perl">        <span class="p">};</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="68" 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="LC68" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$@</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="69" 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="LC69" class="line" lang="perl">            <span class="nb" style="color: #0086b3;">die</span> <span class="p">"</span><span class="s2" style="color: #d14;">Encountered an error: $@</span><span class="p">";</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="67" 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="70" 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="LC70" class="line" lang="perl">        <span class="p">}</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="67" 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="LC71" class="line" lang="perl">    <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span>                   <span class="c1" style="color: #998; font-style: italic;"># plain accession mumber from more reliable EMBL</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC68" class="line" lang="perl">  <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num new_line old" data-linenumber="72" 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="LC69" class="line" lang="perl">      <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">EMBL</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC70" class="line" lang="perl">      <span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_acc</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="perl">  <span class="p">};</span></span>

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<pre style="margin: 0;">-<span id="LC72" class="line" lang="perl">  </span>

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<td class="diff-line-num new old_line" data-linenumber="73" 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="LC72" class="line" lang="perl">        <span class="nb" style="color: #0086b3;">eval</span> <span class="p">{</span></span>

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<td class="diff-line-num new old_line" data-linenumber="73" 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="LC73" class="line" lang="perl">            <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">SeqIO</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">_load_module</span><span class="p">("</span><span class="s2" style="color: #d14;">Bio::DB::EMBL</span><span class="p">");</span></span>

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="perl">            <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$gb</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;">Bio::DB::</span><span class="nv" style="color: #008080;">EMBL</span><span class="o" style="font-weight: 600;">-></span><span class="k" style="font-weight: 600;">new</span><span class="p">();</span></span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="perl">            <span class="nv" style="color: #008080;">$seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$gb</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">get_Seq_by_acc</span><span class="p">(</span><span class="nv" style="color: #008080;">$file</span><span class="p">);</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="perl">        <span class="p">};</span>   </span>

</pre>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="perl">        <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="vg" style="color: #008080;">$@</span><span class="p">)</span> <span class="p">{</span></span>

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="perl">            <span class="nb" style="color: #0086b3;">die</span> <span class="p">"</span><span class="s2" style="color: #d14;">Encountered an error: $@</span><span class="p">";</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="perl">        <span class="p">}</span>        </span>

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<pre style="margin: 0;"> <span id="LC80" class="line" lang="perl">    <span class="p">}</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="perl">    <span class="k" style="font-weight: 600;">print</span> <span class="bp" style="color: #999;">STDERR</span> <span class="p">"</span><span class="s2" style="color: #d14;">Could not find sequence [</span><span class="si" style="color: #d14;">$file</span><span class="s2" style="color: #d14;">]</span><span class="p">"</span> <span class="o" style="font-weight: 600;">&&</span> <span class="k" style="font-weight: 600;">return</span> <span class="k" style="font-weight: 600;">unless</span> <span class="nv" style="color: #008080;">$seq</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="perl">    <span class="k" style="font-weight: 600;">return</span> <span class="nv" style="color: #008080;">$seq</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="159" 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="166" 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">@@ -159,20 +166,20 @@ sub extract {</td>

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<pre style="margin: 0;"> <span id="LC166" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC167" class="line" lang="perl"> <span class="c1" style="color: #998; font-style: italic;">#build BioPerl sequence objects</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="161" 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="168" 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="LC168" class="line" lang="perl"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nv" style="color: #008080;">$strand</span> <span class="o" style="font-weight: 600;">==</span> <span class="o" style="font-weight: 600;">-</span><span class="mi" style="color: #099;">1</span><span class="p">)</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="162" 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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC162" class="line" lang="perl">     <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$five_prime_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff right">PrimarySeq</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">alphabet</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">dna</span><span class="p">',</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq</span><span class="o" style="font-weight: 600;">=></span><span class="nv" style="color: #008080;">$five_prime</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="163" 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="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC163" class="line" lang="perl">     <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$snp_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff right">PrimarySeq</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">alphabet</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">dna</span><span class="p">',</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq</span><span class="o" style="font-weight: 600;">=></span><span class="nv" style="color: #008080;">$snp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="164" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC164" class="line" lang="perl">     <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$three_prime_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff right">PrimarySeq</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">alphabet</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">dna</span><span class="p">',</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq</span><span class="o" style="font-weight: 600;">=></span><span class="nv" style="color: #008080;">$three_prime</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" 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="169" 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="LC169" class="line" lang="perl">     <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$five_prime_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;"><span class="idiff left">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff">PrimarySeq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="k" style="font-weight: 600;"><span class="idiff right">new</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">alphabet</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">dna</span><span class="p">',</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq</span><span class="o" style="font-weight: 600;">=></span><span class="nv" style="color: #008080;">$five_prime</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" 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="170" 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="LC170" class="line" lang="perl">     <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$snp_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;"><span class="idiff left">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff">PrimarySeq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="k" style="font-weight: 600;"><span class="idiff right">new</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">alphabet</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">dna</span><span class="p">',</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq</span><span class="o" style="font-weight: 600;">=></span><span class="nv" style="color: #008080;">$snp</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="165" 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="171" 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="LC171" class="line" lang="perl">     <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$three_prime_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;"><span class="idiff left">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff">PrimarySeq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="k" style="font-weight: 600;"><span class="idiff right">new</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">alphabet</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">dna</span><span class="p">',</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq</span><span class="o" style="font-weight: 600;">=></span><span class="nv" style="color: #008080;">$three_prime</span><span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="165" 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="172" 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="LC172" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="166" 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="173" 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="LC173" class="line" lang="perl">     <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$str</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$three_prime_seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">revcom</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="167" 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="174" 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="LC174" class="line" lang="perl">         <span class="nv" style="color: #008080;">$snp_seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">revcom</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$five_prime_seq</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">revcom</span><span class="o" style="font-weight: 600;">-></span><span class="nv" style="color: #008080;">seq</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="168" 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="175" 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="LC175" class="line" lang="perl">     <span class="nv" style="color: #008080;">$str</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/ //g</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="169" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="176" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC169" class="line" lang="perl">     <span class="nv" style="color: #008080;">$out_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff">PrimarySeq</span></span><span class="idiff right"> </span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">id</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$fastaid</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="170" 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="176" 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="LC176" class="line" lang="perl">     <span class="nv" style="color: #008080;">$out_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;"><span class="idiff left">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff">PrimarySeq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="k" style="font-weight: 600;"><span class="idiff right">new</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">id</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$fastaid</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="170" 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">

170

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<td class="diff-line-num new_line" data-linenumber="177" 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="LC177" class="line" lang="perl">                                     <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">alphabet</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">dna</span><span class="p">',</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="171" 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">

171

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<td class="diff-line-num new_line" data-linenumber="178" 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">

178

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<pre style="margin: 0;"> <span id="LC178" class="line" lang="perl">                                     <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$str</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="172" 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">

172

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<td class="diff-line-num new_line" data-linenumber="179" 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">

179

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<pre style="margin: 0;"> <span id="LC179" class="line" lang="perl"> <span class="p">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="p">{</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="173" 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">

173

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<td class="diff-line-num new_line" data-linenumber="180" 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">

180

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<pre style="margin: 0;"> <span id="LC180" class="line" lang="perl">     <span class="k" style="font-weight: 600;">my</span> <span class="nv" style="color: #008080;">$str</span> <span class="o" style="font-weight: 600;">=</span> <span class="nv" style="color: #008080;">$five_prime</span><span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$snp</span><span class="o" style="font-weight: 600;">.</span> <span class="p">"</span><span class="s2" style="color: #d14;"> </span><span class="p">"</span><span class="o" style="font-weight: 600;">.</span> <span class="nv" style="color: #008080;">$three_prime</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="174" 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">

174

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<td class="diff-line-num new_line" data-linenumber="181" 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">

181

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<pre style="margin: 0;"> <span id="LC181" class="line" lang="perl">     <span class="nv" style="color: #008080;">$str</span> <span class="o" style="font-weight: 600;">=~</span> <span class="sr" style="color: #009926;">s/ //g</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="175" 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">

175

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<td class="diff-line-num new_line old" data-linenumber="182" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC175" class="line" lang="perl">     <span class="nv" style="color: #008080;">$out_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;"><span class="idiff left">new</span></span><span class="idiff"> </span><span class="nn" style="color: #555;"><span class="idiff">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff">PrimarySeq</span></span><span class="idiff right"> </span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">id</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$fastaid</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="176" 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="182" 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">

182

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<pre style="margin: 0;">+<span id="LC182" class="line" lang="perl">     <span class="nv" style="color: #008080;">$out_seq</span> <span class="o" style="font-weight: 600;">=</span> <span class="nn" style="color: #555;"><span class="idiff left">Bio::</span></span><span class="nv" style="color: #008080;"><span class="idiff">PrimarySeq</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-></span></span><span class="k" style="font-weight: 600;"><span class="idiff right">new</span></span><span class="p">(</span><span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">id</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$fastaid</span><span class="p">,</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="176" 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">

176

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<td class="diff-line-num new_line" data-linenumber="183" 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">

183

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<pre style="margin: 0;"> <span id="LC183" class="line" lang="perl">                                     <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">alphabet</span><span class="o" style="font-weight: 600;">=></span><span class="p">'</span><span class="s1" style="color: #d14;">dna</span><span class="p">',</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="177" 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">

177

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<td class="diff-line-num new_line" data-linenumber="184" 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">

184

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<pre style="margin: 0;"> <span id="LC184" class="line" lang="perl">                                     <span class="o" style="font-weight: 600;">-</span><span class="nv" style="color: #008080;">seq</span> <span class="o" style="font-weight: 600;">=></span> <span class="nv" style="color: #008080;">$str</span> <span class="p">);</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="178" 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="185" 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">

185

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<pre style="margin: 0;"> <span id="LC185" class="line" lang="perl"> <span class="p">}</span></span>

</pre>

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<br>

</li>

<li id="384adeead2ae33537082bc3db4b10a27220e76ca">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#384adeead2ae33537082bc3db4b10a27220e76ca"><strong>dist.ini</strong></a>

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

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

1

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

1

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

<pre style="margin: 0;"> <span id="LC1" class="line" lang="ini"><span class="py">name</span> <span class="p">=</span> <span class="s" style="color: #d14;">Bio-Variation</span></span>

</pre>

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

2

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<td class="diff-line-num new_line old" data-linenumber="2" 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="LC2" class="line" lang="ini"><span class="py">version</span> <span class="p">=</span> <span class="s" style="color: #d14;">1.7.<span class="idiff left right">4</span></span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">

</td>

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

<pre style="margin: 0;">+<span id="LC2" class="line" lang="ini"><span class="py">version</span> <span class="p">=</span> <span class="s" style="color: #d14;">1.7.<span class="idiff left right">5</span></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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<td class="diff-line-num new_line" data-linenumber="3" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

3

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

<pre style="margin: 0;"> <span id="LC3" class="line" lang="ini"><span class="py">author</span> <span class="p">=</span> <span class="s" style="color: #d14;">Allen Day <allenday@ucla.edu></span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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<td class="diff-line-num new_line" data-linenumber="4" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">

4

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

<pre style="margin: 0;"> <span id="LC4" class="line" lang="ini"><span class="py">author</span> <span class="p">=</span> <span class="s" style="color: #d14;">Heikki Lehvaslaiho <heikki@bioperl.org></span></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">

5

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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">

5

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

<pre style="margin: 0;"> <span id="LC5" class="line" lang="ini"><span class="py">copyright_holder</span> <span class="p">=</span> <span class="s" style="color: #d14;">See individual modules</span></span>

</pre>

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<br>

</li>

<li id="860c894f76026ba2f4228857a6ec3699da75dbc9">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#860c894f76026ba2f4228857a6ec3699da75dbc9"><strong>lib/Bio/Variation.pm</strong></a>

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<pre style="margin: 0;"> <span id="LC1" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">Variation</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

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<pre style="margin: 0;"> <span id="LC3" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">utf8</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC4" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC5" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">warnings</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">@@ -7,7 +7,7 @@ use warnings;</td>

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<pre style="margin: 0;"> <span id="LC7" class="line" lang="perl"><span class="mi" style="color: #099;">1</span><span class="p">;</span></span>

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

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># ABSTRACT: BioPerl variation-related functionality</span></span>

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># AUTHOR: <span class="idiff left right">See the individual modules for their authors.</span></span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># AUTHOR: <span class="idiff left right">Heikki Lehväslaiho <heikki-at-bioperl-dot-org></span></span></span>

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<pre style="margin: 0;"> <span id="LC11" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># OWNER: See the individual modules for their copyright holders</span></span>

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<pre style="margin: 0;"> <span id="LC12" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># LICENSE: Perl_5</span></span>

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<pre style="margin: 0;"> <span id="LC13" class="line" lang="perl"></span>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="17" 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">@@ -17,8 +17,21 @@ See L<Bio::Perl> for examples.</td>

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

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<pre style="margin: 0;"> <span id="LC18" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=head1 DESCRIPTION</span></span>

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

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<pre style="margin: 0;">-<span id="LC20" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">The code in this distribution focuses on simple low-dependency variant-related</span></span>

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">functionality for BioPerl. See the specific modules for details.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">These classes are part of "Computational Mutation Expression Toolkit"</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">project at European Bioinformatics Institute</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;"><http://www.ebi.ac.uk/mutations/toolkit/>, but they are written to be</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">as general as possinble.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="perl"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">Bio::Variation name space contains modules to store sequence variation</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">information as differences between the reference sequence and changes</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">sequences. Also included are classes to write out and recrete objects</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">from EMBL-like flat files and XML. Lastly, there are simple classes to</span></span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">calculate values for sequence change objects.</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="perl"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">See "Computational Mutation Expression Toolkit" web pages for more</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">information:</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="perl"></span>

</pre>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">      http://www.ebi.ac.uk/mutations/toolkit/</span></span>

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<pre style="margin: 0;"> <span id="LC35" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC36" class="line" lang="perl"><span class="cm" style="color: #998; font-style: italic;">=cut</span></span>

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<pre style="margin: 0;"> <span id="LC37" class="line" lang="perl"></span>

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<li id="a17d804eb208f51efc62cedddba0dd5fc021066b">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#a17d804eb208f51efc62cedddba0dd5fc021066b"><strong>lib/Bio/Variation/AAChange.pm</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">@@ -100,7 +100,7 @@ methods. Internal methods are usually preceded with a _</td>

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<pre style="margin: 0;"> <span id="LC100" class="line" lang="perl"></span>

</pre>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="102" 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="102" 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="LC102" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">AAChange</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="103" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC103" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::AAChange::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="104" 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="103" 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="LC103" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::AAChange::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" 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="LC104" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">vars</span> <span class="sx" style="color: #d14;">qw($MATRIX)</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" 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="LC105" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" 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="106" 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="LC106" class="line" lang="perl"></span>

</pre>

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<br>

</li>

<li id="fa1ce291cc95312c601c6ffb2b662cddcace940d">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#fa1ce291cc95312c601c6ffb2b662cddcace940d"><strong>lib/Bio/Variation/AAReverseMutate.pm</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="93" 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="93" 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">@@ -93,7 +93,7 @@ methods. Internal methods are usually preceded with a _</td>

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<pre style="margin: 0;"> <span id="LC93" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>

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<td class="diff-line-num old_line" data-linenumber="94" 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="LC94" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="95" 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="LC95" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">AAReverseMutate</span><span class="p">;</span></span>

</pre>

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

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

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<pre style="margin: 0;">-<span id="LC96" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::AAReverseMutate::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="97" 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="96" 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="LC96" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::AAReverseMutate::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="97" 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="97" 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="LC97" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="98" 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="LC98" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="99" 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="99" 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="LC99" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Object preamble - inheritance</span></span>

</pre>

</td>

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<br>

</li>

<li id="1d5e0b89f8a1dab378c4116ab66a3d16ea0c69df">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#1d5e0b89f8a1dab378c4116ab66a3d16ea0c69df"><strong>lib/Bio/Variation/Allele.pm</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="85" 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="85" 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">@@ -85,7 +85,7 @@ methods. Internal methods are usually preceded with a _</td>

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<pre style="margin: 0;"> <span id="LC85" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="86" 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="LC86" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC87" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">Allele</span><span class="p">;</span></span>

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

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<pre style="margin: 0;">-<span id="LC88" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::Allele::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="89" 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="LC88" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::Allele::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

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<pre style="margin: 0;"> <span id="LC89" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC90" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC91" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Object preamble - inheritance</span></span>

</pre>

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<br>

</li>

<li id="37c8b44f7b6a505391243b288a619d7928f06d9d">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#37c8b44f7b6a505391243b288a619d7928f06d9d"><strong>lib/Bio/Variation/DNAMutation.pm</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="97" 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="97" 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">@@ -97,7 +97,7 @@ methods. Internal methods are usually preceded with a _</td>

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<pre style="margin: 0;"> <span id="LC97" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC98" class="line" lang="perl"></span>

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<td class="diff-line-num old_line" data-linenumber="99" 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="LC99" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">DNAMutation</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC100" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::DNAMutation::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::DNAMutation::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

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<pre style="margin: 0;"> <span id="LC101" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="102" 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="LC102" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="103" 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="103" 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="LC103" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Object preamble - inheritance</span></span>

</pre>

</td>

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<br>

</li>

<li id="74ef1fa2d9266baf8d5ee894426f943aa1d70509">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#74ef1fa2d9266baf8d5ee894426f943aa1d70509"><strong>lib/Bio/Variation/IO.pm</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="236" 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="236" 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">@@ -236,7 +236,7 @@ methods. Internal methods are usually preceded with a _</td>

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<pre style="margin: 0;"> <span id="LC236" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>

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<pre style="margin: 0;"> <span id="LC237" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC238" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">IO</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC239" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::IO::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

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<pre style="margin: 0;">+<span id="LC239" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::IO::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

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<pre style="margin: 0;"> <span id="LC240" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC241" class="line" lang="perl"></span>

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<pre style="margin: 0;"> <span id="LC242" class="line" lang="perl"></span>

</pre>

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</li>

<li id="caf6f454b5383691278978fcdadeeaf8e6c533c0">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#caf6f454b5383691278978fcdadeeaf8e6c533c0"><strong>lib/Bio/Variation/IO/flat.pm</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="68" 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="68" 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">@@ -68,7 +68,7 @@ methods. Internal methods are usually preceded with a _</td>

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<pre style="margin: 0;"> <span id="LC68" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>

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<pre style="margin: 0;"> <span id="LC69" class="line" lang="perl"></span>

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<td class="diff-line-num old_line" data-linenumber="70" 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="LC70" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::IO::</span><span class="nv" style="color: #008080;">flat</span><span class="p">;</span></span>

</pre>

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<pre style="margin: 0;">-<span id="LC71" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::IO::flat::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::IO::flat::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

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<pre style="margin: 0;"> <span id="LC72" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC73" class="line" lang="perl"></span>

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<td class="diff-line-num old_line" data-linenumber="74" 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="LC74" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Text::</span><span class="nv" style="color: #008080;">Wrap</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="48a56f92704de7600c65a931a93e4c8900a5e0da">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#48a56f92704de7600c65a931a93e4c8900a5e0da"><strong>lib/Bio/Variation/IO/xml.pm</strong></a>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="77" 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="77" 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">@@ -77,7 +77,7 @@ methods. Internal methods are usually preceded with a _</td>

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<pre style="margin: 0;"> <span id="LC77" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>

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<pre style="margin: 0;"> <span id="LC78" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="79" 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="LC79" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::IO::</span><span class="nv" style="color: #008080;">xml</span><span class="p">;</span></span>

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<pre style="margin: 0;">-<span id="LC80" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::IO::xml::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::IO::xml::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

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<pre style="margin: 0;"> <span id="LC81" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">vars</span> <span class="sx" style="color: #d14;">qw($seqdiff $var $prevdnaobj $prevrnaobj $prevaaobj)</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC82" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

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<pre style="margin: 0;"> <span id="LC83" class="line" lang="perl"></span>

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<li id="a0aabaa3ef3d83b4441855fd5c86502d264a6e7b">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#a0aabaa3ef3d83b4441855fd5c86502d264a6e7b"><strong>lib/Bio/Variation/README</strong>

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

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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">                       README for Bio::Variation classes</span>

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

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

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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">These classes are part of "Computational Mutation Expression Toolkit"</span>

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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">project at European Bioinformatics Institute</span>

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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"><http://www.ebi.ac.uk/mutations/toolkit/>, but they are written to be</span>

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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">as general as possinble.</span>

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

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<pre style="margin: 0;">-<span id="LC10" class="line" lang="plaintext">Bio::Variation name space contains modules to store sequence variation</span>

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<pre style="margin: 0;">-<span id="LC11" class="line" lang="plaintext">information as differences between the reference sequence and changes</span>

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<pre style="margin: 0;">-<span id="LC12" class="line" lang="plaintext">sequences. Also included are classes to write out and recrete objects</span>

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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">from EMBL-like flat files and XML. Lastly, there are simple classes to</span>

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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">calculate values for sequence change objects.</span>

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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>

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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">See "Computational Mutation Expression Toolkit" web pages for more</span>

</pre>

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

17

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

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

</pre>

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<td class="diff-line-num old old_line" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

18

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

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

</pre>

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

19

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

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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext">     http://www.ebi.ac.uk/mutations/toolkit/</span>

</pre>

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

20

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

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

<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"></span>

</pre>

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

21

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

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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"></span>

</pre>

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

22

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

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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext">Send bug reports using the bioperl bug-tracking system at</span>

</pre>

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

23

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

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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext">  https://github.com/bioperl/bioperl-live/issues.</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="24" 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">

24

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

</td>

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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> </span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="25" 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">

25

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

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

<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext">Send general comments, questions, and feature requests to the bioperl</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="26" 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">

26

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

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<pre style="margin: 0;">-<span id="LC26" class="line" lang="plaintext">mailing list:</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="27" 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">

27

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

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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="28" 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">

28

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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext">     bioperl-l@bioperl.org</span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="29" 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">

29

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<pre style="margin: 0;">-<span id="LC29" class="line" lang="plaintext"></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="30" 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="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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

<pre style="margin: 0;">-<span id="LC30" class="line" lang="plaintext">Heikki Lehväslaiho <heikki-at-bioperl-dot-org></span></pre>

</td>

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</table>

<br>

</li>

<li id="bb802b019691ae4bef7db35fce466f358f1fa284">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#bb802b019691ae4bef7db35fce466f358f1fa284"><strong>lib/Bio/Variation/RNAChange.pm</strong></a>

<hr>

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

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="110" 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="110" 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">@@ -110,7 +110,7 @@ methods. Internal methods are usually preceded with a _</td>

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<td class="diff-line-num old_line" data-linenumber="110" 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="110" 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="LC110" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="111" 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="111" 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="LC111" class="line" lang="perl"></span>

</pre>

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

112

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<td class="diff-line-num new_line" data-linenumber="112" 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="LC112" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">RNAChange</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

113

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<td class="diff-line-num new_line old" data-linenumber="113" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC113" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::RNAChange::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="114" 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="113" 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">

113

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::RNAChange::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

</pre>

</td>

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<pre style="margin: 0;"> <span id="LC114" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="115" 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="LC115" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="116" 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="116" 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="LC116" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Object preamble - inheritance</span></span>

</pre>

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<br>

</li>

<li id="789d8a42ca4aba466e884536281e26fa5e9afc97">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#789d8a42ca4aba466e884536281e26fa5e9afc97"><strong>lib/Bio/Variation/SNP.pm</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="61" 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="61" 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">@@ -61,7 +61,7 @@ methods. Internal methods are usually preceded with a _</td>

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<pre style="margin: 0;"> <span id="LC61" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>

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<td class="diff-line-num old_line" data-linenumber="62" 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="LC62" class="line" lang="perl"></span>

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<td class="diff-line-num old_line" data-linenumber="63" 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="LC63" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">SNP</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="64" 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="64" 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="LC64" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::SNP::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="65" 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="64" 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="LC64" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::SNP::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

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<pre style="margin: 0;"> <span id="LC65" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="66" 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="LC66" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">vars</span> <span class="sx" style="color: #d14;">qw($AUTOLOAD)</span><span class="p">;</span></span>

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<td class="diff-line-num old_line" data-linenumber="67" 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="67" 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="LC67" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::Root::</span><span class="nv" style="color: #008080;">Root</span><span class="p">;</span></span>

</pre>

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<br>

</li>

<li id="0d0a9aaab5bb3ce4c26aa129ee6c529d67968a0a">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#0d0a9aaab5bb3ce4c26aa129ee6c529d67968a0a"><strong>lib/Bio/Variation/SeqDiff.pm</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="104" 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="104" 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">@@ -104,7 +104,7 @@ methods. Internal methods are usually preceded with a _</td>

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<td class="diff-line-num new_line" data-linenumber="104" 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="LC104" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Let the code begin...</span></span>

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="106" 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="LC106" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">SeqDiff</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<td class="diff-line-num new_line old" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC107" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::SeqDiff::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="108" 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="107" 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="LC107" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::SeqDiff::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

</pre>

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<pre style="margin: 0;"> <span id="LC108" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

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

109

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109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::Tools::</span><span class="nv" style="color: #008080;">CodonTable</span><span class="p">;</span></span>

</pre>

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

110

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

110

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<pre style="margin: 0;"> <span id="LC110" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nn" style="color: #555;">Bio::</span><span class="nv" style="color: #008080;">PrimarySeq</span><span class="p">;</span></span>

</pre>

</td>

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<br>

</li>

<li id="5a0af526767c1358b8a94a876e6a8263a5053e54">

<a href="https://salsa.debian.org/med-team/libbio-variation-perl/commit/95dd84550fed6915bba79cf09d448dde3a8ed8d0#5a0af526767c1358b8a94a876e6a8263a5053e54"><strong>lib/Bio/Variation/VariantI.pm</strong></a>

<hr>

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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="103" 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="103" 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">@@ -103,7 +103,7 @@ methods. Internal methods are usually preceded with a _</td>

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

103

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103

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<pre style="margin: 0;"> <span id="LC103" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="104" 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">

104

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104

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<pre style="margin: 0;"> <span id="LC104" class="line" lang="perl"></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="105" 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">

105

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105

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<pre style="margin: 0;"> <span id="LC105" class="line" lang="perl"><span class="nb" style="color: #0086b3;">package</span> <span class="nn" style="color: #555;">Bio::Variation::</span><span class="nv" style="color: #008080;">VariantI</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old old_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

106

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<td class="diff-line-num new_line old" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">

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<pre style="margin: 0;">-<span id="LC106" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::VariantI::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">4</span></span><span class="p">';</span></span>

</pre>

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<td class="diff-line-num new old_line" data-linenumber="107" 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="106" 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="LC106" class="line" lang="perl"><span class="nv" style="color: #008080;">$</span><span class="nn" style="color: #555;">Bio::Variation::VariantI::</span><span class="nv" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="p">'</span><span class="s1" style="color: #d14;">1.7.<span class="idiff left right">5</span></span><span class="p">';</span></span>

</pre>

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

107

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107

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<pre style="margin: 0;"> <span id="LC107" class="line" lang="perl"><span class="k" style="font-weight: 600;">use</span> <span class="nv" style="color: #008080;">strict</span><span class="p">;</span></span>

</pre>

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<td class="diff-line-num old_line" data-linenumber="108" 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="LC108" class="line" lang="perl"><span class="c1" style="color: #998; font-style: italic;"># Object preamble - inheritance</span></span>

</pre>

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

109

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109

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<pre style="margin: 0;"> <span id="LC109" class="line" lang="perl"></span>

</pre>

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