@gmod/jbrowse
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JBrowse - client-side genome browser
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<!DOCTYPE html><html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>Blog · JBrowse</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="A fast, embeddable genome browser built with HTML5 and JavaScript"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="Blog · JBrowse"/><meta property="og:type" content="website"/><meta property="og:url" content="https://jbrowse.org/index.html"/><meta property="og:description" content="A fast, embeddable genome browser built with HTML5 and JavaScript"/><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 Blog ATOM Feed"/><link rel="alternate" type="application/rss+xml" href="https://jbrowse.org/blog/feed.xml" title="JBrowse Blog RSS Feed"/><script type="text/javascript" src="https://buttons.github.io/buttons.js"></script><link rel="stylesheet" href="/css/main.css"/></head><body class="blog"><div class="fixedHeaderContainer"><div class="headerWrapper wrapper"><header><a href="/"><h2 class="headerTitle">JBrowse</h2></a><div class="navigationWrapper navigationSlider"><nav class="slidingNav"><ul class="nav-site nav-site-internal"><li class="siteNavGroupActive siteNavItemActive"><a href="/blog" target="_self">Blog</a></li><li class=""><a href="/docs/installation.html" target="_self">Documentation</a></li><li class=""><a href="/en/demos.html" target="_self">Demos</a></li><li class=""><a href="/en/developers.html" target="_self">Developers</a></li><li class=""><a href="/en/contact.html" target="_self">Contact</a></li><li class=""><a href="/en/references.html" target="_self">References</a></li><li class=""><a href="/en/help.html" target="_self">Help</a></li></ul></nav></div></header></div></div><div class="navPusher"><div class="docMainWrapper wrapper"><div class="container docsNavContainer" id="docsNav"><nav class="toc"><div class="toggleNav"><section class="navWrapper wrapper"><div class="navBreadcrumb wrapper"><div class="navToggle" id="navToggler"><i></i></div><h2><i>›</i><span>All Blog Posts</span></h2><div class="tocToggler" id="tocToggler"><i class="icon-toc"></i></div></div><div class="navGroups"><div class="navGroup"><h3 class="navGroupCategoryTitle">All Blog Posts</h3><ul><li class="navListItem"><a class="navItem" href="/blog/2019/07/11/jbrowse-1-16-6.html">JBrowse 1.16.6 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2019/06/12/jbrowse-1-16-5.html">JBrowse 1.16.5 maintenance release</a></li><li class="navListItem"><a class="navItem" href="/blog/2019/04/10/jbrowse-1-16-4.html">JBrowse 1.16.4 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"><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/1.15.1-release/JBrowse-1.15.1.zip">JBrowse-1.15.1.zip</a> - 3.2M
file SHA1 71284c64391798cb2b6648bac125522af1ba17a2</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.1-release/JBrowse-1.15.1-dev.zip">JBrowse-1.15.1-dev.zip</a> - 9.4M
file SHA1 26ccaf7768209fa18e2706ea050fc3f8349ba18d</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.1-release/JBrowse-1.15.1-desktop-win32-x64.zip">JBrowse-1.15.1-desktop-win32-x64.zip</a> - 68M
file SHA1 231934c5813bd02710db42e017a0455652559f45</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.1-release/JBrowse-1.15.1-desktop-linux-x64.zip">JBrowse-1.15.1-desktop-linux-x64.zip</a> - 66M
file SHA1 d895966abbbe2c2d623be6bb5150bb20d0bdc16e</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.1-release/JBrowse-1.15.1-desktop-darwin-x64.zip">JBrowse-1.15.1-desktop-darwin-x64.zip</a> - 66M
file SHA1 bf4429998ae005ff2003e19c461e46d1ebd95a0a</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><p>Add a internal code attribute for XHR requests that use byte-range headers so that if a
server does not support it, an error is returned immediately. Thanks to <a href="https://github.com/theChinster">@theChinster</a>
for the motivating example (<a href="https://github.com/gmod/jbrowse/issues/1131">issue #1131</a>, <a href="https://github.com/gmod/jbrowse/issues/1132">issue #1132</a>, <a href="https://github.com/gmod/jbrowse/pull/1134">issue #1134</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>).</p></li>
<li><p>Speed up TwoBit file processing with a robust implementation of the file spec. The
improvements are contained in a new npm module <a href="https://www.npmjs.com/package/@gmod/twobit">@gmod/twobit</a>.
Thanks to <a href="https://github.com/cmdcolin">@cmdcolin</a> for some testing and motivating examples. (<a href="https://github.com/gmod/jbrowse/issues/1116">issue #1116</a>, <a href="https://github.com/gmod/jbrowse/pull/1146">issue #1146</a>,
<a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Added feature.get('seq') to CRAM features which enables detailed comparison of the
read versus the reference with the renderAlignment configuration. (<a href="https://github.com/gmod/jbrowse/issues/1126">issue #1126</a>,
<a href="https://github.com/gmod/jbrowse/pull/1149">issue #1149</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Added support for 1000genomes CRAM 2.0 codecs via updates to the <a href="https://github.com/gmod">@gmod</a>/cram npm module.
(<a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Add some better formatting for rich metadata in the "About this track" dialog boxes for
tracks. Thanks to Wojtek Bażant for the idea and implementation! (<a href="https://github.com/gmod/jbrowse/pull/1148">issue #1148</a>, <a href="https://github.com/wbazant">@wbazant</a>)</p></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><p>Fix bug where prepare-refseqs with indexed FASTA would allows scrolling past the end of
the chromosome (<a href="https://github.com/cmdcolin">@cmdcolin</a>).</p></li>
<li><p>Fix long standing bug related to not being able to configure dataRoot in the config file.
Now you can set dataRoot=mydirectory to make JBrowse load mydirectory instead of the
default <code>data</code> by default (<a href="https://github.com/gmod/jbrowse/issues/627">issue #627</a>, <a href="https://github.com/gmod/jbrowse/pull/1144">issue #1144</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>).</p></li>
<li><p>Added hashing of the BAM feature data to generate unique IDs in order to distinguish
reads that have nearly identical information (same read name, start, end, seq, etc).
If the reads literally have identical information in them JBrowse is still unable to
display but this generally seems to be due to limited use case such as secondary
alignments in RNA-seq (<a href="https://github.com/gmod/jbrowse/issues/1108">issue #1108</a>, <a href="https://github.com/gmod/jbrowse/pull/1145">issue #1145</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a 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></h1><p class="post-meta">July 19, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.15.0 has been released! This is a really big one.</p>
<p>At long last, JBrowse can open and view CRAM v2 and v3 files just like BAM. In fact, viewing CRAM files can sometimes be even faster than viewing BAM files, because there is less data to move around! Enjoy CRAM support, we all worked really hard to bring it to you! Getting started with CRAM is easy, just use the <code>JBrowse/Store/SeqFeature/CRAM</code> store and the <code>Alignments2</code> track type, just as you probably are already with BAM files. It works with local files too, of course!</p>
<p>Another big development, JBrowse Desktop has matured to the point where we can recommend it without reservation to those looking for a fast, easy to use desktop genome browser for local and remote files. From now on, we'll be publishing builds of JBrowse Desktop for Windows, Mac OS, and Linux alongside the regular JBrowse releases. Download it and give it a try, let us know what you think! Huge congratulations to Colin Diesh (who is now a full-time JBrowse developer!) for thinking of this, and seeing this amazing development through. I think you will be quite pleased with how well JBrowse runs on the desktop!</p>
<p>Also, JBrowse now supports CSI format indexes for BAM fiels and Tabix-indexed (VCF, GFF3, etc) files. Now your BAM files can be even bigger. As if they weren't huge enough already. This continues our very serious commitment to make JBrowse effortlessly usable on even the biggest datasets.</p>
<p>Lastly, JBrowse now sports a nice new text-searching interface accessible from the View → Search menu item in the top bar. This was a cool idea that came out of discussions last month at the <a href="https://galaxyproject.org/events/gccbosc2018/collaboration/">GCCBOSC 2018 CollaborationFest</a>, and was executed with alacrity by Colin!</p>
<p>As always, read on below the fold for the full release notes, including minor improvements and bugfixes. And thanks for using JBrowse. 😁</p>
<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/1.15.0-release/JBrowse-1.15.0.zip">JBrowse-1.15.0.zip</a> - 3.1M
file SHA1 1899fb9fd83738e5c2985517222d80667fec840f</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.0-release/JBrowse-1.15.0-dev.zip">JBrowse-1.15.0-dev.zip</a> - 8.5M
file SHA1 e3cc637b1e90c641a8ca1caf8878a8d3ba9c50ab</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.0-release/JBrowse-1.15.0-desktop-win32-x64.zip">JBrowse-1.15.0-desktop-win32-x64.zip</a> - 68M
file SHA1 1e088e3cbf94194bcf73ebbc8c03e6f2e59e0829</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.0-release/JBrowse-1.15.0-desktop-linux-x64.zip">JBrowse-1.15.0-desktop-linux-x64.zip</a> - 66M
file SHA1 4cdb1a6c65cff0831b982b34e1113fde8c5cb649</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.0-release/JBrowse-1.15.0-desktop-darwin-x64.zip">JBrowse-1.15.0-desktop-darwin-x64.zip</a> - 66M
file SHA1 06c22218d8d37355a0d8ea2084c3dea847bc249c</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="major-improvements"></a><a href="#major-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>Major improvements</h2>
<ul>
<li>Added support for displaying alignments from CRAM files, using the new npm module [@gmod](<a href="https://www.npmjs.com/package/">https://www.npmjs.com/package/</a><a href=)/cram"><a href="https://github.com/gmod">@gmod</a>/cram. Thanks to <a href="https://github.com/keiranmraine">@keiranmraine</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>, <a href="https://github.com/nathanhaigh">@nathanhaigh</a>, and the authors of <code>htslib</code> and <code>htsjdk</code> for invaluable test data and suggestions during this major effort. (<a href="https://github.com/gmod/jbrowse/issues/546">issue #546</a>, <a href="https://github.com/gmod/jbrowse/pull/1120">issue #1120</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Added support for the CSI index format for tabix VCF/BED/GFF and BAM files! This allows
individual chromosomes longer than ~537MB (2<sup>29</sup> bases) to be used in JBrowse. To enable,
use the <code>csiUrlTemplate</code> config to point to the file. The "Open track" dialog also allows
CSI to be used. Thanks to Keiran Raine for initial report and Nathan S Watson-Haigh for
catching a bug in the initial implementation! (<a href="https://github.com/gmod/jbrowse/issues/926">issue #926</a>, <a href="https://github.com/gmod/jbrowse/pull/1086">issue #1086</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Added a new search dialog box via the View->Search features menubar. It will search the
currently configured store for features. You can also configure the dialog class in the
configuration with <code>names.dialog</code> entry, or disable search dialog with <code>disableSearch</code>.
Thanks to the #GCCBOSC hackathon for the idea and feedback (<a href="https://github.com/gmod/jbrowse/pull/1101">issue #1101</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>).</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>Re-enabled JBrowse Desktop builds for releases! The Windows, Mac, and Linux binaries for
JBrowse Desktop are uploaded automatically to GitHub releases page. JBrowse Desktop is a
standalone app that can be used without a web server, similar to IGV or IGB (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Added a <code>dontRedispatch</code> option for GFF3Tabix stores. Example: set <code>dontRedispatch=region</code>
if there are very large <code>region</code> biotype features in the GFF that do not have subfeatures which will
speed up loading times significantly (<a href="https://github.com/gmod/jbrowse/issues/1076">issue #1076</a>, <a href="https://github.com/gmod/jbrowse/pull/1084">issue #1084</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Add auto-lower-casing to the feature.get('...') function, commonly used for callback
customizations. Now, for example, feature.get('ID') works as well as feature.get('id').
Thanks to <a href="https://github.com/nvteja">@nvteja</a> for motivating this! (<a href="https://github.com/gmod/jbrowse/issues/1068">issue #1068</a>, <a href="https://github.com/gmod/jbrowse/pull/1074">issue #1074</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Added cache-busting for track config files which actively prevents stale configuration files
from being loaded (<a href="https://github.com/gmod/jbrowse/pull/1080">issue #1080</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Added indexing of both Name and ID from GFF3Tabix files from generate-names.pl. Thanks to
<a href="https://github.com/billzt">@billzt</a> for the implementation! (<a href="https://github.com/gmod/jbrowse/issues/1069">issue #1069</a>)</li>
<li>Made the color of the guanine (G) residue more orangey than yellow to help visibility.
Thanks to Keiran Raine for the implementation! (<a href="https://github.com/gmod/jbrowse/issues/1079">issue #1079</a>)</li>
<li>Refactored NeatCanvasFeatures and NeatHTMLFeatures as track types. You can enable the track
style on specific tracks instead of globally this way by modifying the track type to be
<code>NeatCanvasFeatures/View/Track/NeatFeatures</code> or <code>NeatHTMLFeatures/View/Track/NeatFeatures</code>.
(<a href="https://github.com/gmod/jbrowse/pull/889">issue #889</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>).</li>
<li>In the location box, allow strings with format ctgA:1-100 e.g. with a hyphen instead of <code>..</code>.
Big thanks to Nathan S Watson-Haigh for the idea and implementation! The default display
remains <code>..</code> but <code>-</code> is allowed. (<a href="https://github.com/gmod/jbrowse/issues/1100">issue #1100</a>, <a href="https://github.com/gmod/jbrowse/pull/1102">issue #1102</a>, <a href="https://github.com/nathanhaigh">@nathanhaigh</a>)</li>
<li>Allow sequences with a colon in their name to be used in the location box. This includes
the HLA reference sequences in hg38. Thanks again to Nathan S Watson-Haigh for the
implementation of this feature. (<a href="https://github.com/gmod/jbrowse/pull/1119">issue #1119</a>, <a href="https://github.com/nathanhaigh">@nathanhaigh</a>)</li>
<li>Fix sensitivity to .gff.gz vs .gff3.gz in GFF3Tabix tracks opened via the "Open track"
dialog for GFF3Tabix. (<a href="https://github.com/gmod/jbrowse/issues/1125">issue #1125</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Feature detail dialog boxes now display subfeatures of features on the reverse strand in
upstream-to-downstream order, instead of in genomic coordinate order. Thanks to
<a href="https://github.com/nathanhaigh">@nathanhaigh</a> for suggesting this and contributing the fix! (<a href="https://github.com/gmod/jbrowse/issues/1071">issue #1071</a>, <a href="https://github.com/gmod/jbrowse/pull/1114">issue #1114</a>, <a href="https://github.com/nathanhaigh">@nathanhaigh</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 potential cross-site-scripting (XSS) vulnerability by disallowing <code>dataRoot</code> config
values or <code>?data=</code> URL parameters that point to a different server from the one serving
JBrowse. Users can disable this security check by setting <code>allowCrossOriginDataRoot = true</code>
in their configuration. (<a href="https://github.com/cmdcolin">@cmdcolin</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Fixed a memory leak that was introduced in JBrowse 1.13.1 in generate-names.pl. Thanks to
<a href="https://github.com/scottcain">@scottcain</a> for reporting (<a href="https://github.com/gmod/jbrowse/issues/1058">issue #1058</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fix the error checking in setup.sh if no node is installed at all (<a href="https://github.com/gmod/jbrowse/pull/1083">issue #1083</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fix calculation of histograms on GFF3 and GFF3Tabix stores. Thanks to <a href="https://github.com/thomasvangurp">@thomasvangurp</a> for
the bug report and sample data! (<a href="https://github.com/gmod/jbrowse/issues/1103">issue #1103</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fix the representation of array-valued attributes in column 9 for GFF3Tabix. Thanks to
<a href="https://github.com/loraine-gueguen">@loraine-gueguen</a> for the bug report! (<a href="https://github.com/gmod/jbrowse/issues/1122">issue #1122</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fixed a bug in which visibleRegion() in GenomeView.js sometimes returned a non-integer value for <code>end</code>, which interfered with some scripts and plugins. Thanks to <a href="https://github.com/rdhayes">@rdhayes</a> for noticing and contributing the fix! (<a href="https://github.com/gmod/jbrowse/issues/491">issue #491</a>, <a href="https://github.com/rdhayes">@rdhayes</a>)</li>
<li>Fixed bug where reference sequences with names containing the <code>:</code> character could not be switched to by typing their name in the search box. (<a href="https://github.com/gmod/jbrowse/issues/1118">issue #1118</a>, <a href="https://github.com/gmod/jbrowse/pull/1119">issue #1119</a>, <a href="https://github.com/nathanhaigh">@nathanhaigh</a>)</li>
<li>Fixed <code>setup.sh</code> behavior when <code>node</code> is not installed, printing a decent error message. (<a href="https://github.com/gmod/jbrowse/issues/1082">issue #1082</a>, <a href="https://github.com/gmod/jbrowse/pull/1083">issue #1083</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2018/06/04/jbrowse-1-14-2-index.html">JBrowse 1.14.2 maintenance release</a></h1><p class="post-meta">June 4, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.14.2 has been released!</p>
<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/1.14.2-release/JBrowse-1.14.2.zip" title="download JBrowse-1.14.2.zip">JBrowse-1.14.2.zip</a> - 2.8M
file SHA1 77c28aa4e00b93b1f1e72c5071aee77e7eaa7baa</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.14.2-release/JBrowse-1.14.2-dev.zip" title="download JBrowse-1.14.2-dev.zip">JBrowse-1.14.2-dev.zip</a> - 7.5M
file SHA1 63b8e0bd8f3ae1f67e6a2e88ce514507a2e756d9</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><p>Added a <code>datasetSelectorWidth</code> configuration key that sets the width of the dataset
selector. The width defaults to <code>15em</code>. Example setting in tracks.conf:
<code>[GENERAL] classicMenu = true datasetSelectorWidth = 20em</code>
Thanks to <a href="https://github.com/srobb1">@srobb1</a> for pointing out the need for this. (<a href="https://github.com/gmod/jbrowse/issues/1059">issue #1059</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>When exporting GFF3 from the 'Save track data' menu, the <code>##sequence-region</code> pragma now
specifies the exact sequence region that was exported from the UI. Thanks to <a href="https://github.com/mwdavis2">@mwdavis2</a>
for pointing this out! (<a href="https://github.com/gmod/jbrowse/issues/905">issue #905</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Improved the welcome screen for the desktop version of JBrowse
(<a href="https://github.com/gmod/jbrowse/issues/1045">issue #1045</a>, <a href="https://github.com/gmod/jbrowse/pull/1050">issue #1050</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></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><p>Fixed the <code>--config</code> option for <code>add-bw-track.pl</code>. Although documented in the script's POD,
it was not actually being processed. Thanks to <a href="https://github.com/loraine-gueguen">@loraine-gueguen</a> for noticing it, and for
contributing the fix! (<a href="https://github.com/gmod/jbrowse/issues/1063">issue #1063</a>, <a href="https://github.com/gmod/jbrowse/pull/1064">issue #1064</a>, <a href="https://github.com/loraine-gueguen">@loraine-gueguen</a>)</p></li>
<li><p>Fixed a bug in which setup.sh failed if run twice in a row under some circumstances.
(<a href="https://github.com/gmod/jbrowse/pull/1053">issue #1053</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed a bug in which setup.sh did not accept nodejs version 10 as sufficiently recent.
(<a href="https://github.com/gmod/jbrowse/pull/1048">issue #1048</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed a bug in which the "Loading..." message erroneously appeared at the top of the
dataset-selection page. Many thanks to <a href="https://github.com/srobb1">@srobb1</a> for noticing this and reporting it!
(<a href="https://github.com/gmod/jbrowse/issues/1057">issue #1057</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>JSON syntax errors in the new configuration loading code now have better error messages.
Thanks to <a href="https://github.com/billzt">@billzt</a> for pointing out the need for this! (<a href="https://github.com/gmod/jbrowse/issues/1061">issue #1061</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2018/05/02/jbrowse-1-14-1-maintenance-release-index.html">JBrowse 1.14.1 maintenance release</a></h1><p class="post-meta">May 2, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.14.1 has been released!</p>
<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/1.14.1-release/JBrowse-1.14.1.zip" title="download JBrowse-1.14.1.zip">JBrowse-1.14.1.zip</a> - 2.8M
file SHA1 f41c89826db00afc4b78a37a255aa6b43c3df986</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.14.1-release/JBrowse-1.14.1-dev.zip" title="download JBrowse-1.14.1-dev.zip">JBrowse-1.14.1-dev.zip</a> - 7.5M
file SHA1 5a2e119c08790eb81dc6ae2ac8cf7483093ac9e5</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><p>JBrowse now supports .idx indexes for VCFs that are generated by <code>igvtools</code> or GATK. Currently
only VCF files can be used with this index type, but this could be expanded to other file types
if users are interested. Thanks to <a href="https://github.com/thon-deboer">@thon-deboer</a> for suggesting this! (<a href="https://github.com/gmod/jbrowse/issues/1019">issue #1019</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>The dropdown dataset selector in "classic menu" mode is now a type-ahead combo box, enabling
fast searching through large numbers of datasets. Thanks to <a href="https://github.com/keiranmraine">@keiranmraine</a> for the suggestion!
(<a href="https://github.com/gmod/jbrowse/issues/752">issue #752</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>There is now a new event named <code>/jbrowse/v1/n/tracks/redrawFinished</code> that fires after the
view is refreshed, when all of the visible tracks are finished drawing (or have errored).
Thanks to <a href="https://github.com/scottcain">@scottcain</a> for suggesting this. (<a href="https://github.com/gmod/jbrowse/issues/1027">issue #1027</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Improve the calculation of feature density for GFF3Tabix and add new one for GFF3 in-memory.
Thanks to <a href="https://github.com/hkmoon">@hkmoon</a> for the suggestion! (<a href="https://github.com/gmod/jbrowse/issues/1039">issue #1039</a>, <a href="https://github.com/gmod/jbrowse/issues/913">issue #913</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Re-enabled JBrowse Desktop builds based on automatically building on Travis-CI
(<a href="https://github.com/gmod/jbrowse/issues/1028">issue #1028</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></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><p>Fixed several bugs related to the file-opening dialog's handling of indexed file types
(bam+bai, gz+tbi, etc). Thanks to <a href="https://github.com/sletort">@sletort</a> for submitting the bug report! (<a href="https://github.com/gmod/jbrowse/issues/1033">issue #1033</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>The Perl formatting tools now properly read <code>include</code>-ed configuration files. Thanks to <a href="https://github.com/carrere">@carrere</a>
for pointing out this bug. (<a href="https://github.com/gmod/jbrowse/issues/551">issue #551</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Fixed a bug in which the faceted track selector was nonfunctional in Internet Explorer 11.
(<a href="https://github.com/gmod/jbrowse/issues/1036">issue #1036</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2018/04/18/jbrowse-1-14-0-release-index.html">JBrowse 1.14.0 release - iframe-less embedding, BigBed support</a></h1><p class="post-meta">April 18, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.14.0 has been released!</p>
<p>This release includes two major improvements, the first being that it's no longer strictly necessary to run JBrowse inside an <code><iframe></code> when embedding it in another site or webpage. Big thanks to Lacey Sanderson for championing this feature, and we look forward to working with the Tripal team toward a better JBrowse integration!</p>
<p>The second major improvement is in displaying data from BigBed files. Not only can JBrowse can now open BigBed files both locally, and over the web, but it now natively displays BED-type thick/thin features and feature blocks rather than converting them to GFF3-style feature hierarchies. This makes both BigBed and BED fast and responsive. The new BED glyph will also use each feature's RGB color if it has one.</p>
<p>There are many more features coming that enhance JBrowse's compatibility with UCSC-format data, stay tuned for future JBrowse releases!</p>
<p>As always, read on below the fold for the full release notes, including minor improvements and bugfixes.</p>
<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/1.14.0-release/JBrowse-1.14.0.zip">JBrowse-1.14.0.zip</a> - 2.8M
file SHA1 4538cf147464b52b7edb9bd67a0aff76ba63b3a1</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.14.0-release/JBrowse-1.14.0-dev.zip">JBrowse-1.14.0-dev.zip</a> - 7.1M
file SHA1 2014b264733cf8cf377ec464eb751726384926df</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="major-improvements"></a><a href="#major-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>Major improvements</h2>
<ul>
<li>JBrowse now behaves much better when embedded in a webpage without using an iframe.
See tests/drupal.htm in the JBrowse code for an example of this usage. Thanks to
<a href="https://github.com/laceysanderson">@laceysanderson</a> for her patiently championing this feature all the way through the
long road to completion! (<a href="https://github.com/gmod/jbrowse/issues/777">issue #777</a>, <a href="https://github.com/gmod/jbrowse/pull/844">issue #844</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>There is a new BigBed store type, for opening BigBed files. An example BigBed track configuration:</li>
</ul>
<pre> [tracks.GENCODE]
storeClass = JBrowse/Store/SeqFeature/BigBed
type = CanvasFeatures
urlTemplate = gencode.bb
style.label = gene_name,name,id
style.description = gene_bio_type
</pre>
<ul>
<li>JBrowse now has much better support for UCSC-style BED and BigBed features, via the new BED
glyph type for CanvasFeatures. Rather than rendering a complex feature hierarchy like many
of the other CanvasFeatures glyphs, the BED glyph draws sub-blocks with thick and thin regions,
for compatibility with the UCSC browser. CanvasFeatures will automatically use the
<code>JBrowse/View/FeatureGlyph/UCSC/BED</code> glyph type if a feature has no subfeatures, but has
<code>blockCount</code> or <code>thickStart</code> attributes. This means that, in practice, a BigBed file will
display very well with just the default configuration. Also for compatibility with the UCSC
browser, JBrowse will set a BED feature's background color if one is included in the
feature data (turn this off by setting <code>itemRgb = false</code>).</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>The current dataset name is now displayed in the top right portion of the menu bar.
(<a href="https://github.com/gmod/jbrowse/issues/767">issue #767</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li><code>prepare-refseqs.pl</code> now accepts a <code>--gff-sizes</code> option to allow defining reference
sequence sizes from the <code>##sequence-region</code> directives in a GFF3 file. <a href="https://github.com/rbuels">@rbuels</a></li>
<li>Some store types now support a <code>topLevelFeatures</code> configuration variable, which allows
tracks to treat certain types of features as 'top-level', even the actual track data
has them as children of other features. One common use case for this would be if
you have gene models in a GFF3 structured as gene→mRNA→exon/CDS/UTR, but you want to
display the "mRNA" features as top-level, i.e. ignore the gene container that they are in.
Now you can set <code>topLevelFeatures = mRNA</code> in the track configuration, and the track will
display only "mRNA" features on the top level, ignoring any other existing top-level features,
and ignoring the containing "gene" features. This helps address what seems to be a common
pain point of having to "filter" tabix-formatted GFF3 before using it with Apollo. One
important caveat is that users that configure tracks to use an "out of band" source of
feature density or coverage data, like a separate wiggle file that shows feature density,
will have to make sure that the density data is correct for this filter setting if they
use it. Thanks to <a href="https://github.com/Yating-L">@Yating-L</a>, <a href="https://github.com/nathandunn">@nathandunn</a>, and <a href="https://github.com/cmdcolin">@cmdcolin</a> for valuable discussions.
Stores that support <code>topLevelFeatures</code> currently are: GFF3Tabix, GFF3, BED, BEDTabix,
GTF, and REST (<a href="https://github.com/gmod/jbrowse/issues/974">issue #974</a>, <a href="https://github.com/gmod/jbrowse/issues/969">issue #969</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>JBrowse can now accept additional configuration from a <code>data-config</code> attribute on its
container element. This is useful for embedding JBrowse in other sites, particularly
in cases where the JBrowse assets and configuration are stored or referenced from a
different location from the page displaying the embedded JBrowse. For example:</li>
</ul>
<pre>
<div class="jbrowse"
data-config='"baseUrl": "../jbrowse"'
id="GenomeBrowser"
style="height: 600px; width: 100%; padding: 0; border: 0;"
>
</div>
</pre>
would tell JBrowse to look for its configuration and assets at the relative base URL
"../jbrowse". [@rbuels](https://github.com/rbuels)
* JBrowse now has a favicon! ([issue #973](https://github.com/gmod/jbrowse/issues/973), [@rbuels](https://github.com/rbuels))
* Added additional caching code to SequenceChunks and NCList stores, reducing duplicate
network requests and increasing performance in some circumstances ([issue #855](https://github.com/gmod/jbrowse/pull/855), [@cmdcolin](https://github.com/cmdcolin))
<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>Fix a bug in which saving exported data to a file was nonfunctional for some export
data types. <a href="https://github.com/rbuels">@rbuels</a></li>
<li>Fix a bug in which subfeatures were not always fetched correctly when using the GFF3Tabix
store (<a href="https://github.com/gmod/jbrowse/issues/780">issue #780</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Fixed several bugs with specific cases of relative URLs used in configuration. <a href="https://github.com/rbuels">@rbuels</a></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2018/03/28/jbrowse-1-13-1-maintenance-release-index.html">JBrowse 1.13.1 maintenance release</a></h1><p class="post-meta">March 28, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.13.1 has been released!</p>
<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/1.13.1-release/JBrowse-1.13.1.zip" title="download JBrowse-1.13.1.zip">JBrowse-1.13.1.zip</a> - 2.7M
file SHA1 a22df76b7e970af9c7c6bda36ebdc4181344dbfd</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.13.1-release/JBrowse-1.13.1-dev.zip" title="download JBrowse-1.13.1-dev.zip">JBrowse-1.13.1-dev.zip</a> - 6.4M
file SHA1 686d04a3e0a07c70b62b8cd3ebe0741853971b03</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><p>Gene, ProcessedTranscript, and Segments glyphs can now render third-level subfeatures
(such as <code>stop_codon_read_through</code> features) as simple boxes that draw on top of the
main segment glyph. Thanks to <a href="https://github.com/mpoelchau">@mpoelchau</a> for pointing out the need for this!
(<a href="https://github.com/gmod/jbrowse/issues/584">issue #584</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>CanvasFeatures tracks, when guessing which glyph to show for a feature in a track
that does not specify glyphs in its configuration, will now use a Segments glyph
instead of a Box glyph if the feature in question has subfeatures, and is not
otherwise recognized as a gene or processed transcript. <a href="https://github.com/rbuels">@rbuels</a></p></li>
<li><p>Added a check in the <code>setup.sh</code> script for NodeJS >= 6 and NPM >= 3.
(<a href="https://github.com/gmod/jbrowse/issues/1026">issue #1026</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Plugins that don't need CSS can now set <code>jbrowsePlugin.css</code> to <code>false</code> in their
package.json files to prevent JBrowse trying to load their css/main.css file,
if they don't use any CSS. (<a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Add ability for the CanvasFeatures feature labels to stay visible on the screen.
(<a href="https://github.com/gmod/jbrowse/issues/390">issue #390</a>, <a href="https://github.com/gmod/jbrowse/pull/971">issue #971</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Improve VCF tracks support for GVCF generated by GATK, and fix a number of related
VCF details display bugs. (<a href="https://github.com/gmod/jbrowse/pull/991">issue #991</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p><code>generate-names.pl</code> now supports indexing GFF3 files, enabling better use of
GFF3Tabix tracks. Thanks to <a href="https://github.com/billzt">@billzt</a> for the initial implementation!
(<a href="https://github.com/gmod/jbrowse/issues/780">issue #780</a>, <a href="https://github.com/gmod/jbrowse/pull/900">issue #900</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>CanvasFeatures <code>ProcessedTranscript</code> and <code>Gene</code> glyphs now support a "style→utrHeightPercent" configuration variable that sets the percentage of the overall feature's height that UTRs have. This was previously hardcoded to 65, now it is customizable, defaulting to its old value of 65. <a href="https://github.com/rbuels">@rbuels</a></p></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><p>Updated <code>NeatCanvasFeatures</code> and <code>NeatHTMLFeatures</code> plugins to support a <code>gradient</code>
configuration variable, fix rendering of outrons, restore their default
gradient-drawing behavior, disable gradients by default on Alignments and
Alignments2 track types, and clean up their documentation. (<a href="https://github.com/gmod/jbrowse/issues/931">issue #931</a>, <a href="https://github.com/gmod/jbrowse/issues/982">issue #982</a>,
<a href="https://github.com/gmod/jbrowse/issues/985">issue #985</a>, <a href="https://github.com/gmod/jbrowse/issues/931">issue #931</a>, <a href="https://github.com/gmod/jbrowse/issues/992">issue #992</a>, <a href="https://github.com/gmod/jbrowse/pull/1011">issue #1011</a>, <a href="https://github.com/enuggetry">@enuggetry</a>)</p></li>
<li><p>Fixed a bug with plugin loading that was preventing some plugins from working
correctly. (<a href="https://github.com/gmod/jbrowse/issues/1025">issue #1025</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p><code>flatfile-to-json.pl</code> will now refuse to format a track if the trackLabel
contains a '/' character. Thanks to <a href="https://github.com/dytk2134">@dytk2134</a> for pointing this out, and <a href="https://github.com/cmdcolin">@cmdcolin</a>
for the fix! (<a href="https://github.com/gmod/jbrowse/issues/1023">issue #1023</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed a bug in which the viewing location would not be preserved across page reloads
if <code>generate-names.pl</code> had not been run, or a names store had not otherwise
been defined. Thanks to <a href="https://github.com/cmdcolin">@cmdcolin</a> for the bug report. (<a href="https://github.com/gmod/jbrowse/issues/1016">issue #1016</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2018/03/15/jbrowse-1-13-0-release-index.html">JBrowse 1.13.0 release - now with webpack!</a></h1><p class="post-meta">March 15, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I'm pleased to announce that JBrowse 1.13.0 has been released!</p>
<p>There are actually not a huge number of new features in this release, but there has been a significant change in the way JBrowse is built behind the scenes, and the introduction of a slight (slight! I hope it's slight!) backward incompatibility with some existing plugins.</p>
<p>JBrowse now uses webpack to build and package its code for consumption by web browsers, which opens up a lot of options for the development team, paving the way for a much nicer road to all of the great things coming down the road in JBrowse 2. Most importantly, it means that we can build JBrowse 2 with modern technologies, while sharing code (particularly data stores) with JBrowse 1, which should greatly accelerate JBrowse 2 development. Yeah, we're playing 4-D chess here.</p>
<p>However, besides the big build system overhaul, there are also some nice new improvements and bug fixes in this release, read below for the full release notes.</p>
<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/1.13.0-release/JBrowse-1.13.0.zip">JBrowse-1.13.0.zip</a> - 2.7M
file SHA1 4f28b25cb1ec4038723d9afe00f30c7695bee4a1</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.13.0-release/JBrowse-1.13.0-dev.zip">JBrowse-1.13.0-dev.zip</a> - 6.1M
file SHA1 30688686d568f3ff95cd1f603ea1a060835f714b</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="major-improvements"></a><a href="#major-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>Major improvements</h2>
<ul>
<li>JBrowse now uses a Webpack-based build system, which greatly speeds up JBrowse's
initial loading time. More importantly, going forward, this change will also enable us to make much more effective use of the huge node.js ecosystem that has grown up in
recent years, as well as to use newer versions of JavaScript itself while
still maintaining compatibility with older web browsers.</li>
<li>Behind the scenes, the way JBrowse plugins are discovered and loaded has also
changed significantly. The most visible consequence of this change is that
installations that use plugins must now use the JBrowse-1.13.0-dev.zip release
(or check out the <code>master</code> branch from GitHub), and must re-run the webpack build
(most easily by running <code>setup.sh</code>) every time a plugin is added or removed from
JBrowse. Although we think that most users of plugins will not experience any
problems, we recommend that installations that make use of plugins other than the
standard built-in plugins (Neat*Features, RegexSearch, etc) test the compatibility
of their plugins thoroughly before deploying this release, and report any problems
either to the JBrowse issue tracker on GitHub, or to the gmod-ajax mailing list.</li>
<li>Again, concisely: if you use JBrowse plugins other than the "stock" ones that
come with JBrowse, you must now use the <code>dev</code> release of JBrowse, and re-run either
<code>setup.sh</code> or <code>npm run build</code> every time you add or remove a plugin.
(<a href="https://github.com/gmod/jbrowse/issues/981">issue #981</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>JBrowse plugins can now be published and installed with NPM. Simply publish your
plugin using the standard <code>npm publish</code> machinery, and make sure its package name
ends with "-jbrowse-plugin". For example, if you have a plugin named "foo", publish
it to npm as "foo-jbrowse-plugin". However, if your plugin is named MyAwesomePlugin,
which is not compatible with npmjs.org's naming conventions, you will want to publish
it as something like "myawesome-jbrowse-plugin" and add a configuration stanza to its
package.json file telling JBrowse its real plugin name. Example:</li>
</ul>
<pre style="display: block;">{
...
"jbrowsePlugin": {
"name": "MyAwesomePlugin"
},
...
}
</pre>
<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>Added <code>disableCollapsedClick</code> and <code>enableCollapsedMouseover</code> track configuration options.
The <code>enableCollapsedMouseover</code> option is useful when features do not overlap e.g.
chromosome segmentation and <code>disableCollapsedClick</code> is useful when the collapsed features
are very dense. Thanks to <a href="https://github.com/rdhayes">@rdhayes</a> for tips (<a href="https://github.com/gmod/jbrowse/issues/544">issue #544</a>, <a href="https://github.com/gmod/jbrowse/pull/870">issue #870</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Removed JBrowse 1.2.1 compatibility. Please use JBrowse 1.12.5 or earlier
if you still have old data formatted with JBrowse 1.2.1. (<a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>For <code>npm</code> installations of JBrowse, jb_run.js and jb_setup.js are now installed into
the standard <code>node_modules/.bin</code> location. (<a href="https://github.com/gmod/jbrowse/issues/1021">issue #1021</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 bug in which adding setting <code>tracklabels=0</code> in the URL failed to hide
track labels when <code>nav=0</code> was also set in the URL. Thanks to Vaneet Lotay for reporting
the problem, and <a href="https://github.com/cmdcolin">@cmdcolin</a> for the fix. (<a href="https://github.com/gmod/jbrowse/issues/1017">issue #1017</a>, <a href="https://github.com/gmod/jbrowse/pull/1018">issue #1018</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2018/02/28/jbrowse-1-12-5-maintenance-release-index.html">JBrowse 1.12.5 maintenance release</a></h1><p class="post-meta">February 28, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.12.5 has been released!</p>
<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>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2018/02/14/jbrowse-1-12-4-maintenance-release-index.html">JBrowse 1.12.4 maintenance release</a></h1><p class="post-meta">February 14, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.12.4 has been released, with a great many improvements and bugfixes! Apologies for the long delay since the last release.</p>
<p>One highlight of this release is that we have fixed a severe incompatibility that prevented many of the JBrowse formatting scripts from running correctly on Perl 5.18 and above.</p>
<p>However, there have been a HUGE number of smaller improvements and bugfixes, have a look at the release notes below!</p>
<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/1.12.4-release/JBrowse-1.12.4.zip">JBrowse-1.12.4.zip</a> - 5.7M
file SHA1 9c3b88d982ceb86de9999e49ddde631d6b41a28f</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.12.4-release/JBrowse-1.12.4-dev.zip">JBrowse-1.12.4-dev.zip</a> - 30M
file SHA1 bb3fa872cbc57055712114e3e01cdcad6776a3b6</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>Fixed SEVERE performance regression that basically made flatfile-to-json.pl
unusable on Perl 5.18 and higher. Huge thanks to Colin Diesh for tracking
this down. (<a href="https://github.com/gmod/jbrowse/issues/470">issue #470</a>, <a href="https://github.com/gmod/jbrowse/pull/912">issue #912</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Added code to calculate feature density histograms for Tabix-indexed GFF3
(<code>GFF3Tabix</code>) data sources. Thanks to <a href="https://github.com/nathandunn">@nathandunn</a> for noticing and fixing
this! (<a href="https://github.com/gmod/jbrowse/pull/956">issue #956</a>, <a href="https://github.com/nathandunn">@nathandunn</a>)</li>
<li>Added a new "Hide unspliced reads" menu item to Alignments and Alignments2
tracks that filter out reads that have no <code>N</code>s in their CIGAR strings.
Thanks to Deepak Kunni and Nathan Dunn for their work on this.
(<a href="https://github.com/gmod/jbrowse/pull/921">issue #921</a>, <a href="https://github.com/deepakunni3">@deepakunni3</a>)</li>
<li>setup.sh now uses npm instead of Bower (which is deprecated) to install
dependencies. <a href="https://github.com/enuggetry">@enuggetry</a></li>
<li>Removed legacy <code>wig-to-json.pl</code> and <code>bam-to-json.pl</code> scripts. <a href="https://github.com/rbuels">@rbuels</a></li>
<li>Added a <code>--trackConfig</code> option to <code>prepare-refseqs.pl</code> to allow injecting
refseq configuration variables at format time. (<a href="https://github.com/gmod/jbrowse/pull/884">issue #884</a>, <a href="https://github.com/erasche">@erasche</a>)</li>
<li>Added trackLabels: "no-block" config feature. Moves track labels/menus
above the features so as not to obscure the features. (<a href="https://github.com/gmod/jbrowse/issues/901">issue #901</a>, #490)</li>
<li>Added a <code>--category</code> option to <code>add-bw-track.pl</code> and <code>add-bam-track.pl</code> to
set the new track's category. Thanks to <a href="https://github.com/loraine">@loraine</a>-gueguen for the implementation!
(<a href="https://github.com/gmod/jbrowse/pull/911">issue #911</a>, <a href="https://github.com/loraine">@loraine</a>-gueguen)</li>
<li>Made jbrowse installable using <code>npm</code>. <a href="https://github.com/cmdcolin">@cmdcolin</a> and <a href="https://github.com/enuggetry">@enuggetry</a>.</li>
<li>Implemented a built-in node.js Express server <code>jb_run.js</code> for quick JBrowse launching.
<a href="https://github.com/enuggetry">@enuggetry</a></li>
<li>Added an <code>--unsorted</code> option to <code>prepare-refseqs.pl</code> that formats reference sequences
in the same order in which they appear in the input sequence file. Thanks to
<a href="https://github.com/dsenalik">@dsenalik</a> for the suggestion and implementation! (<a href="https://github.com/gmod/jbrowse/pull/924">issue #924</a>, <a href="https://github.com/dsenalik">@dsenalik</a>)</li>
<li>Allows for dot-notation instead of JSON (<a href="https://github.com/gmod/jbrowse/pull/952">issue #952</a>) for addTracks, addBookmarks,
and addStores. <a href="https://github.com/GMOD/jbrowse/pull/952">https://github.com/GMOD/jbrowse/pull/952</a>. Address security concerns
adding JSON to GET (<a href="https://nvd.nist.gov/vuln/detail/CVE-2016-6816">https://nvd.nist.gov/vuln/detail/CVE-2016-6816</a>) <a href="https://github.com/nathandunn">@nathandunn</a>.</li>
<li>If a track has no <code>key</code> set in its track configuration, JBrowse will now look for
a <code>key</code> in its track metadata, and use that if it is present. Thanks to Loraine
Guéguen for the idea (<a href="https://github.com/gmod/jbrowse/issues/957">issue #957</a>, <a href="https://github.com/gmod/jbrowse/pull/958">issue #958</a>). <a href="https://github.com/rbuels">@rbuels</a></li>
<li>Fixed bug in <code>maker2jbrowse</code> script that allows <code>maker2jbrowse</code> to be installed
in system executable directories, and adds a <code>--sortMem</code> option.
(<a href="https://github.com/gmod/jbrowse/pull/877">issue #877</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fixed a cosmetic/styling bug with malformed DOM structure in feature detail popup
dialogs. Thanks to Erik Rasche for noticing and fixing this! (<a href="https://github.com/gmod/jbrowse/pull/882">issue #882</a>, <a href="https://github.com/erasche">@erasche</a>)</li>
<li>Added a configuration option that can disable JBrowse's behavior of updating the
browser's title text as the view changes. Thanks to Luka Jeran, Primož Hadalin,
and Nathan Dunn for this! (<a href="https://github.com/gmod/jbrowse/pull/904">issue #904</a>, <a href="https://github.com/lukaw3d">@lukaw3d</a>)</li>
<li>Suppress execution of biodb-to-json.pl on sample data while running setup.sh
on MacOS High Sierra with stock Perl due to an issue with the stock Perl having
broken BerkeleyDB integration, which is needed by Bio::DB::SeqFeature::Store,
the main storage engine used by biodb-to-json.pl. Bug was manifesting as the script
running indefinitely and taking all available disk space.
(<a href="https://github.com/gmod/jbrowse/pull/945">issue #945</a>, <a href="https://github.com/gmod/jbrowse/issues/946">issue #946</a>, <a href="https://github.com/deepakunni3">@deepakunni3</a> and <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Mitigate race condition that could sometimes cause duplicate tracks to be shown
when the browser is started with the <code>loc</code> query parameeter set to the name of
a feature. Thanks to Colin Diesh for the fix. (<a href="https://github.com/gmod/jbrowse/issues/567">issue #567</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fixed issue in which JBrowse crashed when negative numbers were supplied for highlight
coordinates in the URL. Thanks to <a href="https://github.com/h2akim">@h2akim</a> for reporting, and <a href="https://github.com/cmdcolin">@cmdcolin</a> for debugging help.
(<a href="https://github.com/gmod/jbrowse/issues/769">issue #769</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Add <code>--config</code> command-line option to <code>add-bw-track.pl</code> and <code>add-bam-track.pl</code>
scripts. Thanks to Chris Childers for suggesting this! (<a href="https://github.com/gmod/jbrowse/issues/620">issue #620</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Fixed a "cannot read property 'offsetLeft'" error when using touch screens without
the old simple track selector active. (<a href="https://github.com/gmod/jbrowse/issues/893">issue #893</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Upgraded to use new Google Analytics API for usage reporting. (<a href="https://github.com/rdhayes">@rdhayes</a>)</li>
<li>Fixed bug in which start/stop codons were sometimes not displayed in the sequence
track at certain zoom levels (<a href="https://github.com/gmod/jbrowse/issues/858">issue #858</a>, pull req #859, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fixed a regression in which the <code>defaultTracks</code> configuration variable was no longer
respected when set to a comma-separated list. (<a href="https://github.com/gmod/jbrowse/issues/892">issue #892</a>, <a href="https://github.com/gmod/jbrowse/pull/896">issue #896</a>, <a href="https://github.com/rdhayes">@rdhayes</a>)</li>
<li>Made a cosmetic change to Alignments track detail popups, changing "Length on ref" to
be displayed as "Seq length on ref", so that it is displayed more usefully next to
"Seq length". Thanks to <a href="https://github.com/colindaven">@colindaven</a> for the suggestion and implementation!
(<a href="https://github.com/gmod/jbrowse/pull/939">issue #939</a>, <a href="https://github.com/colindaven">@colindaven</a>)</li>
<li>Improved the error messages displayed when a JBrowse glyph class fails to load. Thanks
to <a href="https://github.com/scottcain">@scottcain</a> and <a href="https://github.com/cmdcolin">@cmdcolin</a> for tracking down the issue and improving the error
handling! (<a href="https://github.com/gmod/jbrowse/issues/968">issue #968</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Added support for an <code>addFeatures</code> URL query parameter that can inject features from
the URL query string. (<a href="https://github.com/gmod/jbrowse/issues/976">issue #976</a>, <a href="https://github.com/nathandunn">@nathandunn</a>)</li>
<li>Changed the project's <code>git</code> workflow to utilize a <code>dev</code> branch that is separate from
<code>master</code>, with <code>master</code> only being updated when a new release of JBrowse is published.
(<a href="https://github.com/gmod/jbrowse/issues/975">issue #975</a>, <a href="https://github.com/enuggetry">@enuggetry</a>)</li>
<li>Implemented automated deployment of JBrowse releases to GitHub releases and <code>npm</code>.
Thanks to <a href="https://github.com/abretaud">@abretaud</a>, <a href="https://github.com/nathandunn">@nathandunn</a>, <a href="https://github.com/erasche">@erasche</a>, and <a href="https://github.com/cmdcolin">@cmdcolin</a> for valuable discussions.
(<a href="https://github.com/gmod/jbrowse/issues/822">issue #822</a>, <a href="https://github.com/gmod/jbrowse/pull/979">issue #979</a>, <a href="https://github.com/gmod/jbrowse/pull/984">issue #984</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Added a <code>--bigwigCoverage</code> option to <code>add-bam-track.pl</code> to support configuring pregenerated
coverage histograms from the command line. Thanks to <a href="https://github.com/loraine">@loraine</a>-gueguen for the suggestion
and implementation! (<a href="https://github.com/gmod/jbrowse/pull/972">issue #972</a>, <a href="https://github.com/loraine">@loraine</a>-gueguen)</li>
<li>Improved documentation of the <code>CategoryURL</code> plugin. (<a href="https://github.com/gmod/jbrowse/pull/985">issue #985</a>, <a href="https://github.com/enuggetry">@enuggetry</a>)</li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2017/05/02/jbrowse-1-12-3-index.html">JBrowse-1.12.3: Maintenance Release</a></h1><p class="post-meta">May 2, 2017</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>**We are happy to announce JBrowse 1.12.3 release! **</p>
<p>This release includes a lot of improvements and bugfixes and we thank the community for the support. Some great new features include parsers for new file formats including 2bit format, which can be loaded via prepare-refseqs.pl. There are also new parsers for tabix BED files, tabix GFF and IonTorrent BAM files. Some other improvements include a new <code>noFill</code> option to display BigWig tracks as a scatter plot, the <code>cacheMismatches</code> option that improves performance for BAM files with long reads, and many other small improvements and fixes.</p>
<p>In addition, visit the <a href="https://gmod.github.io/jbrowse-registry/">JBrowse Plugin Registry</a> for a collection of great plugins.</p>
<p>Enjoy!</p>
<ul>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.3.zip">JBrowse-1.12.3.zip</a> - 4.9M
file SHA1 a82b308fe22062c2144efed749e7633c3eeee10a</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.3-dev.zip">JBrowse-1.12.3-dev.zip</a> - 26M
file SHA1 e5eda1fe148ed0e5501f31a95f34f77f4f9bd783</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.3-desktop-osx.zip">JBrowse-1.12.3-desktop-osx.zip</a> - 49M (OSX)
file SHA1 27eede348c613837b6b0a0cf91ee0ca5557d693b</li>
<li><a href="http://jbrowse.org/releases/JBrowse-1.12.3-desktop-win.zip">JBrowse-1.12.3-desktop-win.zip</a> - 49M (Windows)
file SHA1 14a8c9a870864462a96d6f52504556e76541e889</li>
<li><a href="https://hub.docker.com/r/jbrowse/gmod-jbrowse/">Docker Image</a></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>Upgraded build system to install dependencies with bower and
updated to dojo 1.9.8 (<a href="https://github.com/gmod/jbrowse/issues/718">issue #718</a>).</li>
<li>Added the ability to load tabix indexed GFF and BED files.
Thanks to Colin Diesh and @zhjilin for contributing (<a href="https://github.com/gmod/jbrowse/issues/670">issue #670</a>).</li>
<li>Added ability to open BED files in the "Open track" user interface
(<a href="https://github.com/gmod/jbrowse/issues/729">issue #729</a>).</li>
<li>Added ability to access SPARQL and other jbrowse data stores via
CORS. Thanks to the WebApollo hackathon and Eric Rasche for
contributing (<a href="https://github.com/gmod/jbrowse/issues/679">issue #679</a>).</li>
<li>Added extra coloring schemes for the Sequence track when using
protein residues. Thanks to Eric Rasche for the idea and
implementation (<a href="https://github.com/gmod/jbrowse/issues/673">issue #673</a>).</li>
<li>Added ability to specify custom exporter classes for the "Save
track data" option, for example, adding exporter code in plugins
(<a href="https://github.com/gmod/jbrowse/issues/682">issue #682</a>).</li>
<li>Added ability to specify custom name store classes via plugins,
which allows plugins to implement their own search functionality
(<a href="https://github.com/gmod/jbrowse/issues/732">issue #732</a>).</li>
<li>Added a timeout for the track feature density calculations which
can aid problems like consistent chunkSizeLimit issues
(<a href="https://github.com/gmod/jbrowse/issues/540">issue #540</a>, <a href="https://github.com/gmod/jbrowse/issues/730">issue #730</a>).</li>
<li>Added an option to specify multiple highlights, or bookmarks,
using the config file, a remote service, or the URL bar
(<a href="https://github.com/gmod/jbrowse/issues/668">issue #668</a>).</li>
<li>Added support for parsing BAM files from IonTorrent (<a href="https://github.com/gmod/jbrowse/issues/782">issue #782</a>,
<a href="https://github.com/gmod/jbrowse/issues/568">issue #568</a>).</li>
<li>Added support for native file access to .2bit files (<a href="https://github.com/gmod/jbrowse/issues/759">issue #759</a>).</li>
<li>Added list of plugins in about box (<a href="https://github.com/gmod/jbrowse/issues/848">issue #848</a>).</li>
<li>Added cacheMismatches option to improve performance when viewing
long-read alignments (<a href="https://github.com/gmod/jbrowse/issues/860">issue #860</a>).</li>
<li>Added subfeatureDetailLevel config item to make View details box
only load subfeatures on demand (<a href="https://github.com/gmod/jbrowse/issues/861">issue #861</a>).</li>
<li>Added ability to draw scatter plot from BigWig tracks. Thanks to
Keiran Raine for the contribution (<a href="https://github.com/gmod/jbrowse/issues/741">issue #741</a>).</li>
<li>Added a fullviewlink option for the URL bar to disable "View full
link" attribute in embedded JBrowse. Thanks to Vivek Krishnakumar
for contributing (<a href="https://github.com/gmod/jbrowse/issues/813">issue #813</a>).</li>
<li>Added URL parameter &tracklabels=0 and config parameter to hide
track labels (<a href="https://github.com/gmod/jbrowse/issues/869">issue #869</a>).</li>
<li>Added renderAlignment option which creates a per-base alignment
view of the read versus the reference (<a href="https://github.com/gmod/jbrowse/issues/795">issue #795</a>).</li>
<li>Added inferCdsParts option which creates CDS subfeatures from a
continuous CDS region for CanvasFeatures glyphs. Thanks to
Vivek Krishnakumar for the contribution (<a href="https://github.com/gmod/jbrowse/issues/872">issue #872</a>).</li>
<li>Added events tracks/focus, tracks/unfocus, allowing for context
switching based on selected track.</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>Made the menu bar widgets centered again (<a href="https://github.com/gmod/jbrowse/issues/680">issue #680</a>).</li>
<li>Fixed error where the sequence track would not load after "Open
sequence file" (<a href="https://github.com/gmod/jbrowse/issues/831">issue #831</a>).</li>
<li>Fixed problem with persistant "Error reading from name store"
message. Thanks to Anthony Bretaudeau for contributing the fix!
(<a href="https://github.com/gmod/jbrowse/issues/820">issue #820</a>).</li>
<li>Reverted to standard eukaryotic codon set.</li>
<li>Fixed issue where saving session in JBrowse Desktop where plugins
were not saved with session.</li>
<li>Fixed an error if there were numerical values being used as label
or description for the CanvasFeatures type tracks. Thanks to
Eric Rasche for reporting (<a href="https://github.com/gmod/jbrowse/issues/673">issue #673</a>).</li>
<li>Fixed some issues where the Gene glyph would not layout some
features correctly. Thanks to Eric Rasche for reporting
(<a href="https://github.com/gmod/jbrowse/issues/686">issue #686</a>).</li>
<li>Fixed an issue with JBrowse Desktop where saving session would not
save the tracks that were not visible.</li>
<li>Added fix when using indexed fasta from prepare-refseqs.pl.
Thanks to @billzt for the report (<a href="https://github.com/gmod/jbrowse/issues/719">issue #719</a>).</li>
<li>Added a fix for an issue where editing the configuration of files
that were opened by a user didn't work. Thanks to @lpryszcz for
the report (<a href="https://github.com/gmod/jbrowse/issues/569">issue #569</a>).</li>
<li>Fixed some inconsistencies where "Open sequence" on file with a
.fasta file extension failed (<a href="https://github.com/gmod/jbrowse/issues/696">issue #696</a>).</li>
<li>Fixed issue where track labels would re-appear during scroll
(<a href="https://github.com/gmod/jbrowse/issues/793">issue #793</a>).</li>
<li>Added handler for click scrolling in genome view. Thanks to
@exogenesys for fixing (<a href="https://github.com/gmod/jbrowse/issues/709">issue #709</a>).</li>
<li>Fixed a rare error that only affected some versions of Chrome
(<a href="https://github.com/gmod/jbrowse/issues/758">issue #758</a>).</li>
<li>Removed linear gradients from some NeatFeatures tracks
(<a href="https://github.com/gmod/jbrowse/issues/721">issue #721</a>).</li>
<li>Fixed issue where saving GFF3 would fail if the source data
was in VCF format (<a href="https://github.com/gmod/jbrowse/issues/800">issue #800</a>).</li>
<li>Fixed issue where there was a mix of plugin declarations
(<a href="https://github.com/gmod/jbrowse/issues/866">issue #866</a>).</li>
</ul>
</span></div></article></div><div class="docs-prevnext"><a class="docs-prev" href="/blog/">← Prev</a><a class="docs-next" href="/blog/page3/">Next →</a></div></div></div></div></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><h5>Docs</h5><a href="/blog">Blog</a><a href="/docs/tutorial.html">Getting Started</a></div><div><h5>Community</h5><a href="https://gitter.im/GMOD/jbrowse">Project Chat</a><a href="https://twitter.com/JBrowseGossip" target="_blank" rel="noreferrer noopener">Twitter</a></div><div><h5>More</h5><a href="https://github.com/GMOD/jbrowse">GitHub</a><a class="github-button" href="https://github.com/GMOD/jbrowse" data-icon="octicon-star" data-count-href="/GMOD/jbrowse/stargazers" data-show-count="true" data-count-aria-label="# stargazers on GitHub" aria-label="Star this project on GitHub">Star</a></div></section><section class="copyright">Copyright © 2019 Evolutionary Software Foundation</section></footer></div></body></html>