@gmod/jbrowse
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JBrowse - client-side genome browser
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<html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>JBrowse 1.12.5 maintenance release · JBrowse</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="JBrowse 1.12.5 has been released!"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="JBrowse 1.12.5 maintenance release · JBrowse"/><meta property="og:type" content="website"/><meta property="og:url" content="https://jbrowse.org/blog/2018/02/28/jbrowse-1-12-5-maintenance-release-index.html"/><meta property="og:description" content="JBrowse 1.12.5 has been released!"/><meta name="twitter:card" content="summary"/><link rel="shortcut icon" href="/img/favicon.ico"/><link rel="stylesheet" href="//cdnjs.cloudflare.com/ajax/libs/highlight.js/9.12.0/styles/default.min.css"/><link rel="alternate" type="application/atom+xml" href="https://jbrowse.org/blog/atom.xml" title="JBrowse 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maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2019/02/20/jbrowse-1-16-3.html">JBrowse 1.16.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2019/01/31/jbrowse-1-16-2.html">JBrowse 1.16.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/12/27/jbrowse-1-16-1.html">JBrowse 1.16.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/12/13/jbrowse-1-16-0.html">JBrowse 1.16.0 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/10/05/jbrowse-1-15-4.html">JBrowse 1.15.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/08/29/jbrowse-1-15-3.html">JBrowse 1.15.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/08/16/jbrowse-1.15.2-maintenance-release-index.html">JBrowse 1.15.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/08/01/jbrowse-1-15-1-index.html">JBrowse 1.15.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/07/19/jbrowse-1-15-0-release-index.html">JBrowse 1.15.0 release - CRAM support, CSI indexes, and on the desktop!</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/06/04/jbrowse-1-14-2-index.html">JBrowse 1.14.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/05/02/jbrowse-1-14-1-maintenance-release-index.html">JBrowse 1.14.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/04/18/jbrowse-1-14-0-release-index.html">JBrowse 1.14.0 release - iframe-less embedding, BigBed support</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/03/28/jbrowse-1-13-1-maintenance-release-index.html">JBrowse 1.13.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/03/15/jbrowse-1-13-0-release-index.html">JBrowse 1.13.0 release - now with webpack!</a></li><li class="navListItem navListItemActive"><a class="navItem" href="/blog/2018/02/28/jbrowse-1-12-5-maintenance-release-index.html">JBrowse 1.12.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2018/02/14/jbrowse-1-12-4-maintenance-release-index.html">JBrowse 1.12.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2017/05/02/jbrowse-1-12-3-index.html">JBrowse-1.12.3: Maintenance Release</a></li><li class="navListItem"><a class="navItem" href="/blog/2016/06/03/gsoc-students-do-cool-jbrowse-projects-index.html">GSoC Students Do Cool JBrowse Projects</a></li><li class="navListItem"><a class="navItem" href="/blog/2016/03/01/jbrowse-1-12-1-index.html">JBrowse-1.12.1: Maintenance Release</a></li><li class="navListItem"><a class="navItem" href="/blog/2016/02/25/state-of-the-browser-2016-index.html">State of the Browser, 2016</a></li><li class="navListItem"><a class="navItem" href="/blog/2015/12/17/jbrowse-1-12-0-index.html">JBrowse-1.12.0: Open new genome from FASTA, in-line refseqs, NeatFeatures, Desktop</a></li><li class="navListItem"><a class="navItem" href="/blog/2015/02/12/jbrowse-1-11-6-index.html">JBrowse-1.11.6 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/09/04/jbrowse-1-11-5-index.html">JBrowse-1.11.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/05/14/jbrowse-1-11-4-maintenance-release-index.html">JBrowse-1.11.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/03/07/jbrowse-1-11-3-index.html">JBrowse 1.11.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/02/12/tutorial-exploring-structural-variation-index.html">Tutorial: exploring structural variation using JBrowse, from the tomato 150+ re-seq project</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/02/10/jbrowse-1-11-2-index.html">JBrowse 1.11.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2014/01/07/jbrowse-1-11-1-index.html">JBrowse 1.11.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/12/19/jbrowse-1-11-0-index.html">JBrowse 1.11.0: hierarchical track selector, easier configuration, summary mode</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/12/10/jbrowse-1-10-12-index.html">JBrowse 1.10.12 maintenance release (please upgrade!)</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/12/03/jbrowse-1-10-11-index.html">JBrowse 1.10.11 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/11/21/jbrowse-1-10-10-index.html">JBrowse 1.10.10 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/11/08/jbrowse-1-10-9-index.html">JBrowse 1.10.9 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/10/25/jbrowse-1-10-8-index.html">JBrowse 1.10.8 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/10/15/jbrowse-1-10-7-index.html">JBrowse 1.10.7 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/10/07/jbrowse-1-10-6-index.html">JBrowse 1.10.6 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/10/03/jbrowse-1-10-5-index.html">JBrowse 1.10.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/09/23/jbrowse-1-10-4-index.html">JBrowse 1.10.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/09/04/jbrowse-1-10-3-index.html">JBrowse 1.10.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/08/15/jbrowse-1-10-2-index.html">JBrowse 1.10.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/08/06/jbrowse-1-10-1-maintenance-release-index.html">JBrowse 1.10.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/07/30/jbrowse-1-10-0-index.html">JBrowse 1.10.0: Combination tracks, better feature tracks, more glyphs, SPARQL support, and track pinning!</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/07/05/jbrowse-1-9-8-index.html">JBrowse 1.9.8 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/07/02/about-jbrowse-version-numbers-index.html">About JBrowse version numbers</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/06/25/jbrowse-1-9-7-maintenance-release-index.html">JBrowse 1.9.7 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/06/18/jbrowse-1-9-6-maintenance-release-index.html">JBrowse 1.9.6 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/06/12/jbrowse-1-9-5-index.html">JBrowse 1.9.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/05/22/jbrowse-1-9-4-index.html">JBrowse 1.9.4 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/05/09/jbrowse-1-9-3-index.html">JBrowse 1.9.3 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/05/02/jbrowse-1-9-2-index.html">JBrowse 1.9.2 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/04/25/jbrowse-1-9-1-index.html">JBrowse 1.9.1 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/04/16/jbrowse-1-9-0-index.html">JBrowse 1.9.0: VCF support, dataset switching, wiggle track dynamic scaling, REST backend</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/02/12/jbrowse-1-8-1-bugfix-release-index.html">JBrowse 1.8.1 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/01/31/jbrowse-1-8-0-index.html">JBrowse 1.8.0: opens local files, new BAM track types, new plugin system</a></li><li class="navListItem"><a class="navItem" href="/blog/2013/01/10/jbrowse-1-7-6-bugfix-release-index.html">JBrowse 1.7.6 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/12/12/jbrowse-1-7-5-bugfix-release-index.html">JBrowse 1.7.5 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/12/06/jbrowse-1-7-4-bugfix-release-index.html">JBrowse 1.7.4 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/11/28/jbrowse-1-7-3-bugfix-release-index.html">JBrowse 1.7.3 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/11/09/jbrowse-1-7-2-bugfix-release-index.html">JBrowse 1.7.2 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/11/07/jbrowse-1-7-1-bugfix-release-index.html">JBrowse 1.7.1 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/11/05/jbrowse-1-7-0-index.html">JBrowse 1.7.0, now with data export, direct BAM display, and much more</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/10/26/jbrowse-1-6-5-bugfix-release-index.html">JBrowse 1.6.5 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/10/16/jbrowse-1-6-4-bugfix-release-index.html">JBrowse 1.6.4 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/09/28/jbrowse-1-6-3-bugfix-release-index.html">JBrowse 1.6.3 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/09/10/jbrowse-1-6-2-bugfix-release-index.html">JBrowse 1.6.2 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/09/07/rbuels-and-jbrowse-at-the-semantic-web-biohackathon-2012-index.html">@rbuels and JBrowse at the Semantic Web BioHackathon 2012</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/08/28/jbrowse-1-6-1-bugfix-release-index.html">JBrowse 1.6.1 bugfix release</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/08/25/jbrowse-1-6-0-released-includes-feature-descriptions-and-more-index.html">JBrowse 1.6.0 released, includes feature descriptions and more!</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/08/13/jbrowse-1-5-0-released-includes-direct-bigwig-access-index.html">JBrowse 1.5.0 released, includes direct BigWig access!</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/07/12/jbrowse-1-4-2-released-index.html">JBrowse 1.4.2 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/07/10/jbrowse-1-4-1-released-index.html">JBrowse 1.4.1 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/06/14/jbrowse-1-4-0-released-includes-faceted-track-selection-index.html">JBrowse 1.4.0 released, includes faceted track selection!</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/05/07/poliovirus-xrate-demo-by-oscar-westesson-index.html">Poliovirus / XRate demo by Oscar Westesson</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/04/19/jbrowse-1-3-1-released-index.html">JBrowse 1.3.1 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/04/13/jbrowse-1-3-0-index.html">JBrowse 1.3.0, a major release!</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/03/25/jbrowse-1-2-2-released-index.html">JBrowse 1.2.2 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/03/22/hg19-tarball-updated-to-jbrowse-1-2-1-index.html">hg19 tarball updated to JBrowse 1.2.1</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/03/16/jbrowse-in-google-summer-of-code-2012-2-index.html">JBrowse in Google Summer of Code 2012</a></li><li class="navListItem"><a class="navItem" href="/blog/2012/01/13/new-jbrowse-lead-developer-index.html">New JBrowse Lead Developer</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/09/16/dna-sequencing-on-your-iphone-theres-an-app-for-that-index.html">DNA sequencing on your iPhone? There's an app for that</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/09/15/jbrowse-conference-call-index.html">JBrowse conference call</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/08/03/summer-2011-update-index.html">Summer 2011 update</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/04/06/jbrowse-is-hiring-index.html">JBrowse is hiring!</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/03/17/jbrowse-1-2-1-released-index.html">JBrowse 1.2.1 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2011/02/17/jbrowse-1-2-released-index.html">JBrowse 1.2 released</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/12/18/touch-the-genome-index.html">Touch the genome</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/11/24/hg19-tarball-updated-index.html">hg19 tarball updated</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/11/11/data-mini-release-hg19-annotation-tarball-index.html">JBrowse tarball for hg19 human genome data</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/10/11/personal-genomics-website-using-jbrowse-index.html">Personal genomics website using JBrowse</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/10/11/jbrowse-website-moved-to-amazon-cloud-index.html">JBrowse website moved to Amazon cloud</a></li><li class="navListItem"><a class="navItem" href="/blog/2010/09/09/jbrowse-1-1-release-index.html">JBrowse 1.1 release</a></li></ul></div></div></section></div><script>
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<h2><a class="anchor" aria-hidden="true" id="files-for-download"></a><a href="#files-for-download" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Files for download</h2>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.12.5-release/JBrowse-1.12.5.zip" title="download JBrowse-1.12.4.zip">JBrowse-1.12.5.zip</a> - 5.7M
file SHA19c98ff3939459253011fc3f1922a4de7fd48feda</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.12.5-release/JBrowse-1.12.5-dev.zip" title="download JBrowse-1.12.4-dev.zip">JBrowse-1.12.5-dev.zip</a> - 30M
file SHA1 97ab15f5ad5f3d29b2789e8cff077bf3a9684b86</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="minor-improvements"></a><a href="#minor-improvements" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Minor improvements</h2>
<ul>
<li>Safari versions 10 and 11 will now see buttons for downloading feature FASTA
sequences, as well as other sequences. These were turned off for all Safari
browsers back when no version of Safari could download a client-generated file,
but Safari 10 and 11 support it now. Thanks to <a href="https://github.com/kkara">@kkara</a> for noticing the button
was missing and prodding us to look into it. (<a href="https://github.com/gmod/jbrowse/issues/714">issue #714</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Changed the default color for HTMLFeatures features to be a darker gray that
is easier to see. Many thanks to <a href="https://github.com/colindaven">@colindaven</a> for the fix! (<a href="https://github.com/gmod/jbrowse/pull/980">issue #980</a>, <a href="https://github.com/colindaven">@colindaven</a>)</li>
<li>Added the ability to manually specify a reference sequence ordering in the
configuration. Users can now set <code>refSeqOrder: "by_list"</code> and then set
<code>refSeqOrderList: "ctgX,ctgY,ctgZ"</code> to manually specify an ordering.
Thanks to <a href="https://github.com/dsenalik">@dsenalik</a>, <a href="https://github.com/liub1993">@liub1993</a>, <a href="https://github.com/wkpalan">@wkpalan</a>, and <a href="https://github.com/cmdcolin">@cmdcolin</a> for valuable
discussions about this, and <a href="https://github.com/rdhayes">@rdhayes</a> for the prototype implementation.
(<a href="https://github.com/gmod/jbrowse/issues/867">issue #867</a>, <a href="https://github.com/gmod/jbrowse/issues/919">issue #919</a>, <a href="https://github.com/gmod/jbrowse/pull/1007">issue #1007</a>, <a href="https://github.com/rdhayes">@rdhayes</a>)</li>
<li>Added a <code>--noSort</code> option to <code>prepare-refseqs.pl</code> that preserves the reference
sequence ordering in the input file, instead of sorting the reference sequences
alphabetically in the JSON. Thanks to <a href="https://github.com/dsenalik">@dsenalik</a> for the prototype implementation
of this, and <a href="https://github.com/cmdcolin">@cmdcolin</a> and <a href="https://github.com/rdhayes">@rdhayes</a> for valuable discussions.
(<a href="https://github.com/gmod/jbrowse/issues/925">issue #925</a>, <a href="https://github.com/gmod/jbrowse/pull/924">issue #924</a>, <a href="https://github.com/gmod/jbrowse/pull/1007">issue #1007</a>, <a href="https://github.com/dsenalik">@dsenalik</a>)</li>
<li>Feature tracks now support a <code>showNoteInAttributes</code> flag that force the feature's
<code>Notes</code> attribute to be displayed as a regular attribute in the feature detail
popup. This is to support the case in which users want the blue description text
on a feature to be different from the feature's <code>Notes</code> attribute, but still display
the <code>Notes</code> attribute in the detail dialog. Thanks to <a href="https://github.com/loraine-gueguen">@loraine-gueguen</a> and <a href="https://github.com/cmdcolin">@cmdcolin</a>
for the idea and the implementation. (<a href="https://github.com/gmod/jbrowse/pull/885">issue #885</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>When users click on an item in the dropdown autocompletion for the browser search
box, the browser will go directly to that item immediately, eliminating the extra
step of the user having to click "Go". Many thanks to <a href="https://github.com/enuggetry">@enuggetry</a> for noticing the
opportunity for this nice usability enhancement! (<a href="https://github.com/gmod/jbrowse/issues/616">issue #616</a>, <a href="https://github.com/gmod/jbrowse/pull/1001">issue #1001</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>The global <code>highResolutionMode</code> configuration is now set to <code>auto</code>, meaning that
JBrowse by default will now auto-detect high-DPI displays (Apple Retina displays
and similar) and draw canvas-based tracks more clearly on them. This capability
has been present in the JBrowse code for a long time, but has been turned off
by default. (<a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Added support for two new configuration variables for SNPCoverage tracks:
<code>indicatorProp</code> and <code>indicatorDepth</code>, which set the minimum proportion (indicatorProp)
and minimum depth (indicatorDepth) of alternative alleles required to render the
SNP indicator below a SNPCoverage track. Big thanks to Nathan Haigh for the idea
and implementation! (<a href="https://github.com/gmod/jbrowse/pull/951">issue #951</a>, <a href="https://github.com/nathanhaigh">@nathanhaigh</a>)</li>
<li>Added a basic loading screen for when the page is initially loading (<a href="https://github.com/gmod/jbrowse/pull/1008">issue #1008</a>,
<a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>The <code>subfeatureDetailLevel</code> configuration variable for tracks now defaults to a value
of 2, meaning that the builtin JBrowse default feature detail popup dialogs will only
show one level of subfeatures by default. Most feature tracks have only one level of
subfeatures anyway, but for very complex data (like gene models with many transcripts,
each with many introns and exons), this new default will prevent a rather confusing
problem some users were seeing in which JBrowse would seem to 'hang' when clicking a
gene model to see its details. Thanks to <a href="https://github.com/cmdcolin">@cmdcolin</a> for the original implementation of the
<code>subfeatureDetailLevel</code> configuration variable, <a href="https://github.com/kshefchek">@kshefchek</a> for a good bug report that
shows it, and <a href="https://github.com/nathandunn">@nathandunn</a> and <a href="https://github.com/selewis">@selewis</a> for valuable discussions.
(<a href="https://github.com/gmod/jbrowse/issues/559">issue #559</a>, <a href="https://github.com/gmod/jbrowse/pull/1010">issue #1010</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="bug-fixes"></a><a href="#bug-fixes" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Bug fixes</h2>
<ul>
<li>Fixed a security issue with JBrowse error messages. Thanks to <a href="https://github.com/GrainGenes">@GrainGenes</a> for
noticing and reporting it! (<a href="https://github.com/gmod/jbrowse/issues/602">issue #602</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Fixed an off-by-one error in the "Next segment position" field of BAM features.
Thanks to <a href="https://github.com/keiranmraine">@keiranmraine</a> for reporting it, and <a href="https://github.com/rdhayes">@rdhayes</a> for tracking down the fix!
(<a href="https://github.com/gmod/jbrowse/issues/907">issue #907</a>, <a href="https://github.com/gmod/jbrowse/pull/986">issue #986</a>, <a href="https://github.com/rdhayes">@rdhayes</a>)</li>
<li>Fixed the broken demo track data source in the modENCODE sample data. Thanks
to <a href="https://github.com/cmdcolin">@cmdcolin</a> for the fix! (<a href="https://github.com/gmod/jbrowse/pull/999">issue #999</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fixed bug in which dragging an Alignments or Alignments2 track into a combination
track caused the combination track to crash. (<a href="https://github.com/gmod/jbrowse/issues/771">issue #771</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Feature detail dialogs for variant tracks now correctly display "no-call" in
the genotype details table for "./." alleles. Thanks to <a href="https://github.com/carrere">@carrere</a> for reporting
it, and <a href="https://github.com/cmdcolin">@cmdcolin</a> for the fix. (<a href="https://github.com/gmod/jbrowse/issues/980">issue #980</a>, <a href="https://github.com/gmod/jbrowse/pull/990">issue #990</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fix parsing of the END field in VCF tracks, enabling things like CNV and deletion
variants to be visualized from variant tracks. (<a href="https://github.com/gmod/jbrowse/pull/847">issue #847</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fixed a long-standing bug in JBrowse configuration template parsing that
prevented use of dot-notation nested variable names, e.g. <code>{foo.bar}</code>, in
JBrowse configuration, as well as whitespace inside the braces. Big thanks to
<a href="https://github.com/wuroger">@wuroger</a> for finding this bug. (<a href="https://github.com/gmod/jbrowse/issues/1012">issue #1012</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
</ul>
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