@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,