@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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This is a small release that adds a fix for side-scrolling on Macs, where the touchpad would trigger the browsers back action.</p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.6-release/JBrowse-1.16.6.zip">JBrowse-1.16.6.zip</a> - minified release</li>
<li><a href="https://github.com/GMOD/jbrowse/archive/1.16.6-release.zip">JBrowse-1.16.6-dev.zip</a> - use this if you modify jbrowse source code or use plugins</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.6-release/JBrowse-1.16.6-desktop-win32-x64.zip">JBrowse-1.16.6-desktop-win32-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.6-release/JBrowse-1.16.6-desktop-linux-x64.zip">JBrowse-1.16.6-desktop-linux-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.6-release/JBrowse-1.16.6-desktop-darwin-x64.zip">JBrowse-1.16.6-desktop-darwin-x64.zip</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><p>Add name regularization for drosophila style chromsome naming so that
2L maps to chr2L and vice versa (<a href="https://github.com/scottcain">@scottcain</a>)</p></li>
<li><p>Add ability to index names in a BEDTabix file, enabled by default.
Thanks to <a href="https://github.com/billzt">@billzt</a> for the idea and implementation (<a href="https://github.com/gmod/jbrowse/pull/1393">issue #1393</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>Fix the side scrolling on Mac misbehaving and triggering the browser's
back action (a bug that existed only in 1.16.5). Thanks to <a href="https://github.com/nathandunn">@nathandunn</a>
for debugging (<a href="https://github.com/gmod/jbrowse/issues/1397">issue #1397</a>)</li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2019/06/12/jbrowse-1-16-5.html">JBrowse 1.16.5 maintenance release</a></h1><p class="post-meta">June 12, 2019</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I am pleased to announce the release of JBrowse 1.16.5. This includes some name regularization fixes (e.g. when you have chr1 and 1 it tries to map to the same thing), some bigwig fixes, a small speedup for BAM data, and more. Please read the release notes!</p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5.zip">JBrowse-1.16.5.zip</a> - minified release</li>
<li><a href="https://github.com/GMOD/jbrowse/archive/1.16.5-release.zip">JBrowse-1.16.5-dev.zip</a> - use this if you modify jbrowse source code or use plugins</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5-desktop-win32-x64.zip">JBrowse-1.16.5-desktop-win32-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5-desktop-linux-x64.zip">JBrowse-1.16.5-desktop-linux-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.5-release/JBrowse-1.16.5-desktop-darwin-x64.zip">JBrowse-1.16.5-desktop-darwin-x64.zip</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><p>Added better error reporting if there is a BAI file for a genome that
is longer than 2^29 and requires a CSI index</p></li>
<li><p>Added default dontRedispatch=chromosome,region which avoids long
GFF3Tabix redispatching for common gff3 types that don't need it.</p></li>
<li><p>Added a <code>hideIframeDialogUrl</code> option to hide the iframe url in a
<code>iframeDialog</code> popup. Thanks to <a href="https://github.com/mictadlo">@mictadlo</a> for the suggestion (issue
#1365)</p></li>
<li><p>Updated <a href="https://github.com/gmod">@gmod</a>/tabix and <a href="https://github.com/gmod">@gmod</a>/bam to unzip bgzf chunks as they are
received instead of performing chunk merges. This also allows
actual fileOffset to be used as a feature ID instead of CRC32 hash
(<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added regularization of chromosome names using roman numerals,
common in both S. cerevisiae and C. elegans genome communities.
Thanks to <a href="https://github.com/scottcain">@scottcain</a> for assistance (<a href="https://github.com/gmod/jbrowse/pull/1376">issue #1376</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added ability for vertical scroll events to bubble out of the jbrowse
div or iframe, which can be more intuitive in embedded jbrowse's.
Otherwise, the GenomeView stopped all vertical scroll events in it's
area. If you need the old behavior use <code>alwaysStopScrollBubble</code>.
(<a href="https://github.com/cmdcolin">@cmdcolin</a>, <a href="https://github.com/gmod/jbrowse/pull/1373">issue #1373</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 a long standing issue with BigWig files not accessing the
lowest summary zoom level (e.g. the first one after unzoomed).
(<a href="https://github.com/cmdcolin">@cmdcolin</a>, <a href="https://github.com/gmod/jbrowse/issues/1359">issue #1359</a>)</p></li>
<li><p>Fixed a bug with using the scoreType: maxScore configuration on
Wiggle tracks failing at non-summary zoom levels. Thanks to
<a href="https://github.com/patrickcng90">@patrickcng90</a> for reporting</p></li>
<li><p>Fixed a bug with name regularizing that particularly affected CRAM
on mitochondrial chromosomes. Thanks to <a href="https://github.com/sachalau">@sachalau</a> for patience and
sample data for debugging this issue! (<a href="https://github.com/gmod/jbrowse/issues/1367">issue #1367</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue with GFF3/Tabix types colliding their attribute names
with the field e.g. if start=0 was in column 9. Thanks to
<a href="https://github.com/loraine-gueguen">@loraine-gueguen</a> for reporting (<a href="https://github.com/gmod/jbrowse/issues/1364">issue #1364</a>).</p></li>
<li><p>Fixed an issue with NeatHTMLFeatures when zoomed out. Thanks to
<a href="https://github.com/abretaud">@abretaud</a> for the implementation and fix (<a href="https://github.com/gmod/jbrowse/pull/1368">issue #1368</a>).</p></li>
<li><p>Restored ability to access widest zoom level from bigwig. Thanks
to <a href="https://github.com/lukaw3d">@lukaw3d</a> for noticing and debugging (<a href="https://github.com/gmod/jbrowse/issues/1375">issue #1375</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed some minor parsing of 'b' type data series in CRAM files,
which happens when CRAM is not using reference based compression
so it is uncommon (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added some more checks for track types for combination tracks (issue
#1361)</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2019/04/10/jbrowse-1-16-4.html">JBrowse 1.16.4 maintenance release</a></h1><p class="post-meta">April 10, 2019</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I'm pleased to announce the release of JBrowse 1.16.4. This has a couple of specialized fixes.</p>
<p>One fix provides a better error message if you give improper inputs for tabix or BAI files that actually require CSI indexes. This came up often for people in the wheat genome.</p>
<p>Another helps display multiple transcript features for a gene top level feature from HTMLFeatures</p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.4-release/JBrowse-1.16.4.zip">JBrowse-1.16.4.zip</a> - minified release</li>
<li><a href="https://github.com/GMOD/jbrowse/archive/1.16.4-release.zip">JBrowse-1.16.4-dev.zip</a> - use this if you modify jbrowse source code or use plugins</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.4-release/JBrowse-1.16.4-desktop-win32-x64.zip">JBrowse-1.16.4-desktop-win32-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.4-release/JBrowse-1.16.4-desktop-linux-x64.zip">JBrowse-1.16.4-desktop-linux-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.4-release/JBrowse-1.16.4-desktop-darwin-x64.zip">JBrowse-1.16.4-desktop-darwin-x64.zip</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><p>Added <code>indexedFeatures</code> tracklist attribute for GFF3Tabix track types
which controls the feature types from a GFF3Tabix file that are
indexed. Thanks to <a href="https://github.com/loraine-gueguen">@loraine-gueguen</a> for the idea and implementation!
(<a href="https://github.com/gmod/jbrowse/pull/1337">issue #1337</a>, <a href="https://github.com/loraine-guegen">@loraine-guegen</a>)</p></li>
<li><p>Added <code>inferHTMLSubfeatures</code> which automatically creates multiple
mRNA transcripts from a single gene parent feature. Thanks to
<a href="https://github.com/abretaud">@abretaud</a> for the idea and implementation! Note that this is enabled
by default now (<a href="https://github.com/gmod/jbrowse/pull/1343">issue #1343</a>, <a href="https://github.com/gmod/jbrowse/pull/1340">issue #1340</a>)</p></li>
<li><p>Updated jbrowse.org website to run entirely off amazon S3 (<a href="https://github.com/gmod/jbrowse/pull/1347">issue #1347</a>,
<a href="https://github.com/gmod/jbrowse/pull/1348">issue #1348</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>Added better error reporting to GFF3Tabix tracks for if a parsing
error occured. Thanks to <a href="https://github.com/nathanhaigh">@nathanhaigh</a> for reporting (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added fix for VCF that don't contain alternative alleles (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added better error handling if there is a case where a tabix file is
loaded that is on a genome longer than 2^29. CSI indexes are needed for
this. Old versions of tabix which hadn't invented CSI would generate
invalid tabix indexes in this case. Thanks to Hans Vasquez-Gross for
reporting (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed link in documentation. Thanks <a href="https://github.com/agarciamontoro">@agarciamontoro</a> (<a href="https://github.com/gmod/jbrowse/pull/1341">issue #1341</a>)</p></li>
<li><p>Fixed issue with ucsc-to-json.pl creating subfeatures with the wrong
strand. Thanks to <a href="https://github.com/sachalau">@sachalau</a> for finding and fixing (<a href="https://github.com/gmod/jbrowse/pull/1346">issue #1346</a>)</p></li>
</ul>
</span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2019/02/20/jbrowse-1-16-3.html">JBrowse 1.16.3 maintenance release</a></h1><p class="post-meta">February 20, 2019</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>Hello all, this is a small maintenance release that most importantly addresses compatibility that was causing <a href="http://setup.sh">setup.sh</a> to fail on many installations by fixing a missing BioPerl package that was removed from their core distribution. If you are stuck with an older JBrowse release, please follow instructions listed here <a href="https://github.com/GMOD/jbrowse/issues/1313">https://github.com/GMOD/jbrowse/issues/1313</a></p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.3-release/JBrowse-1.16.3.zip">JBrowse-1.16.3.zip</a> - minified release</li>
<li><a href="https://github.com/GMOD/jbrowse/archive/1.16.3-release.zip">JBrowse-1.16.3-dev.zip</a> - use this if you modify jbrowse source code or use plugins</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.3-release/JBrowse-1.16.3-desktop-win32-x64.zip">JBrowse-1.16.3-desktop-win32-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.3-release/JBrowse-1.16.3-desktop-linux-x64.zip">JBrowse-1.16.3-desktop-linux-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.3-release/JBrowse-1.16.3-desktop-darwin-x64.zip">JBrowse-1.16.3-desktop-darwin-x64.zip</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><p>Fix BioPerl setup after changes to the BioPerl distribution caused
setup.sh to fail in all past JBrowse versions (<a href="https://github.com/gmod/jbrowse/issues/1310">issue #1310</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fix issue with NeatCanvasFeatures not drawing gradients on some
features. Thanks to <a href="https://github.com/mara-sangiovanni">@mara-sangiovanni</a> for reporting (<a href="https://github.com/gmod/jbrowse/issues/1311">issue #1311</a>,
<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fix issue for exporting GFF3 for some nested attributes by dumping
JSON into the value field. Thanks to <a href="https://github.com/dionnezaal">@dionnezaal</a> for reporting
(<a href="https://github.com/gmod/jbrowse/issues/1309">issue #1309</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/2019/01/31/jbrowse-1-16-2.html">JBrowse 1.16.2 maintenance release</a></h1><p class="post-meta">January 31, 2019</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I'm happy to announce the release of 1.16.2, it is a smaller maintenance release. It contains several fixes including for CSI in BAM files,
and several other small fixes. Thanks to everyone for communicating requests and bug reports</p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.2-release/JBrowse-1.16.2.zip">JBrowse-1.16.2.zip</a> - minified release</li>
<li><a href="https://github.com/GMOD/jbrowse/archive/1.16.2-release.zip">JBrowse-1.16.2-dev.zip</a> - use this if you modify jbrowse source code or use plugins</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.2-release/JBrowse-1.16.2-desktop-win32-x64.zip">JBrowse-1.16.2-desktop-win32-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.2-release/JBrowse-1.16.2-desktop-linux-x64.zip">JBrowse-1.16.2-desktop-linux-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.2-release/JBrowse-1.16.2-desktop-darwin-x64.zip">JBrowse-1.16.2-desktop-darwin-x64.zip</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><p>Allow configuring the cache busting behavior for adding random ?v= value
to config file requests. This can be configured in index.html. Thanks to
user <a href="https://github.com/sandilyaamit">@sandilyaamit</a> for reporting, this is actually important to disable
when using Amazon presigned URLs (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Adds <code>fixBounds</code> config for XYPlot tracks which can be set to false to
disable the behavior of rounding up or down on the min_score/max_score
variables for the ruler. Thanks to <a href="https://github.com/scottcain">@scottcain</a> for the suggestion
(<a href="https://github.com/gmod/jbrowse/pull/1306">issue #1306</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>Fix ability to use CSI indexes with BAM files since 1.16.0 (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fix ability to read some CRAM files with unmapped mates (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fix issue with the browser loading NaN locations on startup (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Add fix for exporting GFF3 for newer browsers that have Array.values()
enabled. Thanks to Scott Cain for reporting (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Improve error message when refSeqs=file.fai config fails to load
(<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/2018/12/27/jbrowse-1-16-1.html">JBrowse 1.16.1 maintenance release</a></h1><p class="post-meta">December 27, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I'm pleased to announce the release of JBrowse 1.16.1! This release offers a variety of small bugfixes for cross-origin resource fetching, BAM files, and JBrowse desktop.</p>
<p>It also contains a fix that helps very large track lists to have a faster initial load for the Hierarchical track selector specifically.</p>
<p>Enjoy browsing!</p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.1-release/JBrowse-1.16.1.zip">JBrowse-1.16.1.zip</a> - minified release</li>
<li><a href="https://github.com/GMOD/jbrowse/archive/1.16.1-release.zip">JBrowse-1.16.1-dev.zip</a> - use this if you modify jbrowse source code or use plugins</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.1-release/JBrowse-1.16.1-desktop-win32-x64.zip">JBrowse-1.16.1-desktop-win32-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.1-release/JBrowse-1.16.1-desktop-linux-x64.zip">JBrowse-1.16.1-desktop-linux-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.1-release/JBrowse-1.16.1-desktop-darwin-x64.zip">JBrowse-1.16.1-desktop-darwin-x64.zip</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><p>Made a change to make Hierarchical track selector much faster on intial
browser load for very large tracklists (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Updated to webpack 4 for some faster build times (<a href="https://github.com/gmod/jbrowse/pull/1270">issue #1270</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Updated to use dojo/dijit/dojox 1.14 (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Updated NeatCanvasFeatures to allow non-coding transcripts to be colored
differently with <code>style->unprocessedTranscriptColor</code>. Thanks to <a href="https://github.com/billzt">@billzt</a>
for the bug report (<a href="https://github.com/gmod/jbrowse/issues/1298">issue #1298</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 issue where data directories with spaces in them were giving errors
due to CORS on JBrowse Desktop (<a href="https://github.com/gmod/jbrowse/issues/1285">issue #1285</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue where the name store could be queried before being initialized
(<a href="https://github.com/gmod/jbrowse/issues/1286">issue #1286</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed an issue for large BAM headers failing to load post-@gmod/bam
integration (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed access to some cross-origin resources (<a href="https://github.com/gmod/jbrowse/issues/1289">issue #1289</a>, <a href="https://github.com/gmod/jbrowse/pull/1292">issue #1292</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/2018/12/13/jbrowse-1-16-0.html">JBrowse 1.16.0 maintenance release</a></h1><p class="post-meta">December 13, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I am very pleased to announce the release of JBrowse version 1.16.0!</p>
<p>A major new feature of this release is the introduction of paired read visualization options!</p>
<p>And rather than delivering just one type of paired read visualization, there are many options for this including:</p>
<ul>
<li>Pileup - standard alignments view but with connections between pairs</li>
<li>Read cloud - plotting by insert size</li>
<li>Arc view - plotting paired reads as connected arcs</li>
</ul>
<p>There are also multiple coloring options for each type of view, including coloring by insert size (so abnormally large inserts are colored red for example) or pair orientation. Here are some example screenshots to help demonstrate</p>
<p><img src="/img/paired_reads.png" alt=""></p>
<p>Figure 1.standard pileup view with paired and unpaired modes on the same data.</p>
<p><img src="/img/arc_view.png" alt=""></p>
<p>Figure 2. arc view which shows many long-range connections from a mate pair dataset.</p>
<p><img src="/img/read_cloud.png" alt=""></p>
<p>Figure 3. The read cloud view showing color by orientation and size (red being abnormally large insert size, and turquoise and blue being incorrect pair orientations)</p>
<p>JBrowse version 1.16.0 also contains many other features and bug fixes, so please review the changelog below! Also make sure to view the <a href="/docs/paired_reads.html">paired read documentation</a> for more information on the paired read options.</p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.0-release/JBrowse-1.16.0.zip">JBrowse-1.16.0.zip</a> - minified release</li>
<li><a href="https://github.com/GMOD/jbrowse/archive/1.16.0-release.zip">JBrowse-1.16.0-dev.zip</a> - use this if you modify jbrowse source code or use plugins</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.0-release/JBrowse-1.16.0-desktop-win32-x64.zip">JBrowse-1.16.0-desktop-win32-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.0-release/JBrowse-1.16.0-desktop-linux-x64.zip">JBrowse-1.16.0-desktop-linux-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.16.0-release/JBrowse-1.16.0-desktop-darwin-x64.zip">JBrowse-1.16.0-desktop-darwin-x64.zip</a></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 ability to view paired read data as connected entities for BAM and
CRAM store classes. There are multiple different viewing options for this
including plotting by insert size, plotting as connected arcs, or pileup
views for the paired reads. Additonally multiple color schemes are available
for coloring by insert size, pair orientation, mapping quality, and more.
Thanks to <a href="https://github.com/garrettjstevens">@garrettjstevens</a>, <a href="https://github.com/rbuels">@rbuels</a>, <a href="https://github.com/AndyMenzies">@AndyMenzies</a>, and <a href="https://github.com/keiranmraine">@keiranmraine</a> for
testing. Also a big thanks to <a href="https://github.com/jrobinso">@jrobinso</a> from <a href="https://github.com/igvteam">@igvteam</a> for contributions to
CRAM code related to paired reads (<a href="https://github.com/gmod/jbrowse/pull/1235">issue #1235</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><p>For users with the "dev" or compiling JBrowse from source code, the ./setup.sh
now performs a full webpack production build (<a href="https://github.com/gmod/jbrowse/pull/1223">issue #1223</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Created new BAM parsing mechanism using the npm module <a href="https://www.npmjs.com/package/@gmod/bam">@gmod/bam</a>.
Users might see some modest performance improvements due to enhanced tooling.
Thanks to <a href="https://github.com/rbuels">@rbuels</a> and others for testing and feedback (<a href="https://github.com/gmod/jbrowse/pull/1215">issue #1215</a>, <a href="https://github.com/gmod/jbrowse/issues/1178">issue #1178</a>,
<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>setup.sh now supports setting a <code>JBROWSE_PUBLIC_PATH</code> environment variable for
more flexibility in iframeless embedding scenarios (<a href="https://github.com/gmod/jbrowse/issues/1213">issue #1213</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Added support for indexing arbitrary fields from GFF3Tabix files by setting
nameAttributes in the track config e.g. nameAttributes=name,id,customfield.
(<a href="https://github.com/gmod/jbrowse/issues/1115">issue #1115</a>, <a href="https://github.com/gmod/jbrowse/pull/1222">issue #1222</a>, <a href="https://github.com/cmdcolin">@cmdcolin<