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GitLab

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<h3>

Michael R. Crusoe pushed to branch master

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

</h3>

<h4>

Commits:

</h4>

<ul>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbio-graphics-perl/commit/e55f0bc5706009439cafdcc796692e176ba91961">e55f0bc5</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-11-23T08:22:30Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Breaks+Replaces the old libbio-bio-perl

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbio-graphics-perl/commit/f151b2f944c0ea6eced14426841e6ebbd4d1c9e0">f151b2f9</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-11-23T08:35:06Z</i>

</div>

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

</pre>

</li>

<li>

<strong><a href="https://salsa.debian.org/med-team/libbio-graphics-perl/commit/5a52c2185812eab280977b96dcc7a13d9de67534">5a52c218</a></strong>

<div>

<span>by Michael R. Crusoe</span>

<i>at 2019-11-23T08:35:06Z</i>

</div>

<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">release to unstable

</pre>

</li>

</ul>

<h4>4 changed files:</h4>

<ul>

<li class="file-stats">

<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">

debian/changelog

</a>

</li>

<li class="file-stats">

<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

debian/control

</a>

</li>

<li class="file-stats">

<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

debian/patches/series

</a>

</li>

<li class="file-stats">

<a href="#e4c19aed51618bf0c7ebd03189c67e422f84d4eb">

<span class="new-file">

+

debian/patches/spelling

</span>

</a>

</li>

</ul>

<h4>Changes:</h4>

<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">

<a href="https://salsa.debian.org/med-team/libbio-graphics-perl/compare/7d7fce384d211e08e6d3967e4325c5e459740f53...5a52c2185812eab280977b96dcc7a13d9de67534#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>

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1

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">libbio-graphics-perl (2.40-5) unstable; urgency=medium</span>

</pre>

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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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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">  * Team upload.</span>

</pre>

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

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">  * debian/control: Breaks+Replaces the old libbio-bio-perl. (Closes: #942789)</span>

</pre>

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

5

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">  * debian/patches/spelling: fix typos</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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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> -- Michael R. Crusoe <michael.crusoe@gmail.com>  Sat, 23 Nov 2019 09:23:09 +0100</span>

</pre>

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8

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

</pre>

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1

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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">libbio-graphics-perl (2.40-4) unstable; urgency=medium</span>

</pre>

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2

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10

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

</pre>

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3

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<td class="diff-line-num new_line" data-linenumber="11" style="width: 35px; color: rgba(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="LC11" class="line" lang="plaintext">  * Team upload.</span>

</pre>

</td>

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</table>

<br>

</li>

<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">

<a href="https://salsa.debian.org/med-team/libbio-graphics-perl/compare/7d7fce384d211e08e6d3967e4325c5e459740f53...5a52c2185812eab280977b96dcc7a13d9de67534#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>

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

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

<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -28,6 +28,8 @@ Depends: ${perl:Depends},</td>

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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">

28

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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">

28

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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext">         ${misc:Depends},</span>

</pre>

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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">

29

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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">

29

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

</pre>

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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">

30

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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">

30

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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">         libgd-gd2-perl</span>

</pre>

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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">

</td>

<td class="diff-line-num new new_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">

31

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

<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">Breaks: libbio-perl-perl (<< 1.7.3)</span>

</pre>

</td>

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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">

</td>

<td class="diff-line-num new new_line" data-linenumber="32" 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">

32

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Replaces: libbio-perl-perl (<< 1.7.3)</span>

</pre>

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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">

31

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33

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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext">Recommends: libbio-scf-perl,</span>

</pre>

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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext">            perl,</span>

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

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</li>

<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">

<a href="https://salsa.debian.org/med-team/libbio-graphics-perl/compare/7d7fce384d211e08e6d3967e4325c5e459740f53...5a52c2185812eab280977b96dcc7a13d9de67534#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>

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1

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

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

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<li id="e4c19aed51618bf0c7ebd03189c67e422f84d4eb">

<a href="https://salsa.debian.org/med-team/libbio-graphics-perl/compare/7d7fce384d211e08e6d3967e4325c5e459740f53...5a52c2185812eab280977b96dcc7a13d9de67534#e4c19aed51618bf0c7ebd03189c67e422f84d4eb"><strong>debian/patches/spelling</strong></a>

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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">From: Michael R. Crusoe <michael.crusoe@gmail.com></span></span>

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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Subject: Fix a few typos</span></span>

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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/Feature.pm</span></span>

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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/Feature.pm</span></span>

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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">@@ -260,7 +260,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">            called the accession_number. For sequences from established</span>

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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">            databases, the implementors should try to use the correct</span>

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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">            accession number. Notice that primary_id() provides the</span>

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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-           unique id for the implemetation, allowing multiple objects</span></span>

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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+           unique id for the implementation, allowing multiple objects</span></span>

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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff">            to have the same accession number in a particular implementation.</span>

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

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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff">            For sequences with no accession number, this method should return</span>

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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/FeatureFile.pm</span></span>

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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/FeatureFile.pm</span></span>

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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -314,7 +314,7 @@</span></span>

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

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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff">    -safe_world     If the -safe option is not set, and -safe_world</span>

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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff">                    is set to a true value, then Bio::Graphics::FeatureFile</span>

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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-                   will evalute "sub {}" options in a L<Safe::World></span></span>

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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+                   will evaluate "sub {}" options in a L<Safe::World></span></span>

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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff">                    environment with minimum permissions. Subroutines</span>

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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff">                    will be able to access and interrogate </span>

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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff">                    Bio::DB::SeqFeature objects and perform basic Perl</span>

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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/decorated_transcript.pm</span></span>

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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/decorated_transcript.pm</span></span>

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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="p">@@ -17,7 +17,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> sub my_descripton {</span>

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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff">   return <<END;</span>

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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> This glyph extends the functionality of the Bio::Graphics::Glyph::processed_transcript glyph </span>

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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-and allows to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)</span></span>

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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+and allows one to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)</span></span>

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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> on top of gene models. Currently, the glyph can draw decorations in form of colored or outlined boxes </span>

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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> inside or around CDS segments. Protein decorations are specified at the 'mRNA' transcript level </span>

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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> in protein coordinates. Protein coordinates are automatically mapped to nucleotide coordinates by the glyph. </span>

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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -201,7 +201,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff">  return $feature->get_tag_values(DECORATION_TAG_NAME);</span>

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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> }</span>

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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-# allows to retrieve additional decorations via callback</span></span>

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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+# allows one to retrieve additional decorations via callback</span></span>

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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> sub additional_decorations {</span>

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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff">  my $self    = shift;</span>

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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff">  my $feature = $self->feature;</span>

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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -948,7 +948,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> =head1 DESCRIPTION</span>

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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> This glyph extends the functionality of the L<Bio::Graphics::Glyph::processed_transcript> glyph </span>

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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-and allows to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)</span></span>

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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+and allows one to draw protein decorations (e.g., signal peptides, transmembrane domains, protein domains)</span></span>

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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> on top of gene models. Currently, the glyph can draw decorations in form of colored or outlined boxes </span>

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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> inside or around CDS segments. Protein decorations are specified at the 'mRNA' transcript level </span>

</pre>

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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> in protein coordinates. Protein coordinates are automatically mapped to nucleotide coordinates by the glyph. </span>

</pre>

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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/fb_shmiggle.pm</span></span>

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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/fb_shmiggle.pm</span></span>

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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="p">@@ -611,7 +611,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> <br></span>

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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> <br></span>

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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Setting 'subsetsnames' allows to rename subsets (very important as in most cases</span></span>

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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Setting 'subsetsnames' allows one to rename subsets (very important as in most cases</span></span>

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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> workflow names of subsets are unsutable for intelligent data display to end users).</span>

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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> If setting omitted, initial subsets names will be used for display.</span>

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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/heat_map.pm</span></span>

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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/heat_map.pm</span></span>

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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -522,7 +522,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> white->red.</span>

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

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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> For the start_color and end_color options, 140 named webcolors</span>

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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-and their corresponsing RGB hex codes (listed below) are supported.</span></span>

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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+and their corresponding RGB hex codes (listed below) are supported.</span></span>

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

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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff">  steelblue               #4682B4</span>

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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff">  royalblue               #041690</span>

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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/ideogram.pm</span></span>

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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/ideogram.pm</span></span>

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78

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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="p">@@ -298,7 +298,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff">   $self->wipe(@_);</span>

</pre>

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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff">   # For single, unaggregated bands, make the terminal band</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="82" 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="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  # a bit wider to accomodate the arc</span></span>

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<td class="diff-line-num new new_line" data-linenumber="83" 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="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  # a bit wider to accommodate the arc</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="84" 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">

84

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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff">   if ($self->{single}) {</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="85" 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="LC85" class="line" lang="diff">     $x1 -= 5 if $state == 1;</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="86" 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="LC86" class="line" lang="diff">     $x2 += 5 if $state == 0;</span>

</pre>

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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/segments.pm</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/segments.pm</span></span>

</pre>

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<td class="diff-line-num new new_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="LC89" class="line" lang="diff"><span class="p">@@ -1136,7 +1136,7 @@</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> hit() method, and both the source and the target DNA must be</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="91" 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="LC91" class="line" lang="diff"> available.  If you pass the glyph a series of</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="92" 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="LC92" class="line" lang="diff"> Bio::SeqFeature::SimilarityPair objects, then these criteria will be</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="93" 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="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-satisified.</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="94" 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="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+satisfied.</span></span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="95" 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="LC95" class="line" lang="diff"> </span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="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="diff"> Without additional help, this glyph cannot display gapped alignments</span>

</pre>

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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> correctly.  To display gapped alignments, you can use the</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="98" 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="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/Glyph/trace.pm</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/Glyph/trace.pm</span></span>

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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="p">@@ -733,7 +733,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> installed).</span>

</pre>

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

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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="diff"> Until an alignment feature is added to this glyph, the feature start and end</span>

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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-must correspond exactly with the begining and end of the called sequence.</span></span>

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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+must correspond exactly with the beginning and end of the called sequence.</span></span>

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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="diff"> Meaning that even if the starting sequence is poor and doesn't match the</span>

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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> sequence, it must still be included.</span>

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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="p">@@ -883,7 +883,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> </span>

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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> =head1 BUGS AND LIMITATIONS</span>

</pre>

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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> </span>

</pre>

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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-See the L<DESCRIPTION> for an explaination of how to align the trace with the</span></span>

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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+See the L<DESCRIPTION> for an explanation of how to align the trace with the</span></span>

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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> reference.</span>

</pre>

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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="117" 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="LC117" class="line" lang="diff"> The trace looks a little off when the feature is on the negative strand of the</span>

</pre>

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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/Panel.pm</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/Panel.pm</span></span>

</pre>

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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="p">@@ -1710,7 +1710,7 @@</span></span>

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<td class="diff-line-num new new_line" data-linenumber="121" 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="LC121" class="line" lang="diff">   -auto_pad    If "left" or "right" keys are in use  true</span>

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<td class="diff-line-num new new_line" data-linenumber="122" 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="LC122" class="line" lang="diff">                then setting auto_pad to a true value</span>

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<td class="diff-line-num new new_line" data-linenumber="123" 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="LC123" class="line" lang="diff">                will allow the panel to adjust its</span>

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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-               width in order to accomodate the</span></span>

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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+               width in order to accommodate the</span></span>

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<td class="diff-line-num new new_line" data-linenumber="126" 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="LC126" class="line" lang="diff">                length of the longest key.</span>

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<td class="diff-line-num new new_line" data-linenumber="127" 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="LC127" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="128" 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="LC128" class="line" lang="diff">   -empty_tracks What to do when a track is empty.    suppress</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="129" 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="LC129" class="line" lang="diff"><span class="p">@@ -1758,7 +1758,7 @@</span></span>

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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff">                Useful when working with the</span>

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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff">                "image" glyph.</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="132" 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="LC132" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="133" 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="LC133" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-  -truetype    Render text using scaleable vector    false</span></span>

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<td class="diff-line-num new new_line" data-linenumber="134" 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="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+  -truetype    Render text using scalable vector    false</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="135" 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="LC135" class="line" lang="diff">                fonts rather than bitmap fonts.</span>

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<td class="diff-line-num new new_line" data-linenumber="136" 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="LC136" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="137" 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="LC137" class="line" lang="diff">   -image_class To create output in scalable vector</span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="138" 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="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- libbio-graphics-perl.orig/lib/Bio/Graphics/Wiggle/Loader.pm</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="139" 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="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ libbio-graphics-perl/lib/Bio/Graphics/Wiggle/Loader.pm</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="140" 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="LC140" class="line" lang="diff"><span class="p">@@ -101,7 +101,7 @@</span></span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="141" 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">

141

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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> </span>

</pre>

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<td class="diff-line-num new new_line" data-linenumber="142" 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">

142

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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> =back</span>

</pre>

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

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<td class="diff-line-num new new_line" data-linenumber="143" 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">

143

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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> </span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="144" 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">

144

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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-Example entended track declaration:</span></span>

</pre>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="145" 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">

145

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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+Example intended track declaration:</span></span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="146" 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">

146

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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> </span>

</pre>

</td>

</tr>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="147" 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">

147

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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff">  track type=wiggle_0 name="example" description="20 degrees, 2 hr"  \</span>

</pre>

</td>

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

</td>

<td class="diff-line-num new new_line" data-linenumber="148" 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">

148

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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff">        trim=stdev2 transform=logsquared</span></pre>

</td>

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