@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</a>)</p></li>
<li><p>Add support for generate-names to index VCF features that have multiple IDs in
the ID column (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added documentation on embedding JBrowse in an iframe and in a div, including
how to embed JBrowse using a custom JavaScript object as a configuration
(<a href="https://github.com/gmod/jbrowse/pull/1228">issue #1228</a>, <a href="https://github.com/gmod/jbrowse/pull/1243">issue #1243</a>, <a href="https://github.com/rbuels">@rbuels</a> and <a href="https://github.com/garrettjstevens">@garrettjstevens</a>)</p></li>
<li><p>Added ability to render non-coding transcript types to the default Gene glyph
which helps when a gene feature has a mix of coding and non-coding subfeatures
(<a href="https://github.com/gmod/jbrowse/issues/1106">issue #1106</a>, <a href="https://github.com/gmod/jbrowse/pull/1230">issue #1230</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Created new VCF parsing mechanism using the NPM module
<a href="https://www.npmjs.com/package/@gmod/vcf">@gmod/vcf</a>. Thanks to <a href="https://github.com/cmdcolin">@cmdcolin</a> and
others for testing and feedback (<a href="https://github.com/gmod/jbrowse/pull/1227">issue #1227</a>, <a href="https://github.com/gmod/jbrowse/issues/1199">issue #1199</a>, <a href="https://github.com/garrettjstevens">@garrettjstevens</a>)</p></li>
<li><p>Added ability to open "chrom.sizes" files from the Open sequence dialog
(<a href="https://github.com/gmod/jbrowse/issues/1250">issue #1250</a>, <a href="https://github.com/gmod/jbrowse/pull/1257">issue #1257</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added a config <code>datasetLinkToParentIframe</code> to make the dataset selector use
window.parent for when jbrowse is in an iframe (<a href="https://github.com/gmod/jbrowse/pull/1248">issue #1248</a>, <a href="https://github.com/enuggetry">@enuggetry</a>)</p></li>
<li><p>Improved error message that is displayed when a data file cannot be fetched
via CORS (<a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Added some word wrapping for long unbroken fields in the View details
popups. Thanks to <a href="https://github.com/luke-c-sargent">@luke-c-sargent</a> for the idea (<a href="https://github.com/gmod/jbrowse/issues/1246">issue #1246</a>).</p></li>
<li><p>Added <code>hideImproperPairs</code> filter for Alignments2/SNPCoverage tracks which
disambiguates from missing mate pairs (<a href="https://github.com/gmod/jbrowse/pull/1235">issue #1235</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added <code>useTS</code> coloring option for RNA-seq strandedness, similar to the <code>useXS</code>
that existed previously (<a href="https://github.com/gmod/jbrowse/pull/1235">issue #1235</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added a --bgzip_fasta option for prepare-refseqs.pl and also the ability
to index reference sequence names if they are manually specified as a
fasta index e.g. <code>refSeqs=genome.fai</code>. Thanks to <a href="https://github.com/FredericBGA">@FredericBGA</a> for the report!
(<a href="https://github.com/gmod/jbrowse/issues/1281">issue #1281</a>, <a href="https://github.com/gmod/jbrowse/pull/1282">issue #1282</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 some generate-names setups would fail to index features.
Thanks to <a href="https://github.com/BioInfoSuite">@BioInfoSuite</a> for reporting (<a href="https://github.com/gmod/jbrowse/issues/1275">issue #1275</a>, <a href="https://github.com/gmod/jbrowse/pull/1283">issue #1283</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue with getting feature density from BAM files via the index stats
estimation (<a href="https://github.com/gmod/jbrowse/issues/1233">issue #1233</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue where some feature mouseovers where not working properly (issue
#1236, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue where instantiating JBrowse via <code>standalone.js</code> didn't work when
in a production build with JBROWSE_PUBLIC_PATH overridden (<a href="https://github.com/gmod/jbrowse/issues/1239">issue #1239</a>,
<a href="https://github.com/garrettjstevens">@garrettjstevens</a>)</p></li>
<li><p>Small fix for issue where SNPCoverage would crash on some feature filters
(<a href="https://github.com/gmod/jbrowse/issues/1241">issue #1241</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue where JBrowse Desktop was not able to access remote files (issue
#1234, <a href="https://github.com/gmod/jbrowse/pull/1245">issue #1245</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fix issue where the Hierarchical track selector contained a bunch of blank
whitespace. Thanks to <a href="https://github.com/nathanhaigh">@nathanhaigh</a> for reporting! (<a href="https://github.com/gmod/jbrowse/issues/1240">issue #1240</a>, <a href="https://github.com/gmod/jbrowse/pull/1253">issue #1253</a>,
<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue where whitespace surrounding GFF3 attributes and attribute names
was incorporated (<a href="https://github.com/gmod/jbrowse/issues/1221">issue #1221</a>, <a href="https://github.com/gmod/jbrowse/pull/1254">issue #1254</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue with some GFF3Tabix tracks having some inconsistent layout of
features (<a href="https://github.com/gmod/jbrowse/issues/1244">issue #1244</a>, <a href="https://github.com/gmod/jbrowse/pull/1260">issue #1260</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed CRAM store not renaming reference sequences in the same way as other
stores (<a href="https://github.com/gmod/jbrowse/pull/1277">issue #1277</a>, <a href="https://github.com/rbuels">@rbuels</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed bug where older browsers e.g. IE11 were not being properly supported via
babel (<a href="https://github.com/gmod/jbrowse/issues/1259">issue #1259</a>, <a href="https://github.com/gmod/jbrowse/pull/1267">issue #1267</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed bug where some files were not being fetched properly when changing
refseqs. Thanks to <a href="https://github.com/luke-c-sargent">@luke-c-sargent</a> for the report (<a href="https://github.com/gmod/jbrowse/issues/1252">issue #1252</a>)</p></li>
<li><p>Fixed storeTimeout on CRAM files being unused which can result in excessive
fetches (<a href="https://github.com/gmod/jbrowse/pull/1235">issue #1235</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue where JBrowse would load the wrong area of the refseq on startup
resulting in bad layouts and excessive data fetches. Thanks to <a href="https://github.com/hkmoon">@hkmoon</a>,
<a href="https://github.com/cmdcolin">@cmdcolin</a>, and <a href="https://github.com/garrettjstevens">@garrettjstevens</a> for debugging (<a href="https://github.com/gmod/jbrowse/issues/1190">issue #1190</a>, <a href="https://github.com/gmod/jbrowse/pull/1235">issue #1235</a>, pull
#1187)</p></li>
<li><p>Fixed issue where CRAM layout and mouseover would be glitchy due to ID
collisions on features (<a href="https://github.com/gmod/jbrowse/issues/1271">issue #1271</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed parsing of certain bigBed files that were hanging on track startup
(<a href="https://github.com/gmod/jbrowse/issues/1226">issue #1226</a>, <a href="https://github.com/gmod/jbrowse/pull/1229">issue #1229</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue where some parts of a CRAM file would not be displayed in JBrowse
due to a CRAM index parsing issue (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed an issue where BAM features were not lazily evaluating their tags
(<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="notable-changes"></a><a href="#notable-changes" 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>Notable changes</h2>
<ul>
<li>Rendering of features in popups, mouseover tooltips, and feature labels were
made to escape HTML. If you are using literal HTML labels in these places
then set the attribute <code>unsafePopup</code>, <code>unsafeMouseover</code>, or <code>unsafeHTMLFeatures</code>
on your tracks. Thanks to <a href="https://github.com/garrettjstevens">@garrettjstevens</a> (<a href="https://github.com/gmod/jbrowse/pull/1263">issue #1263</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/2018/10/05/jbrowse-1-15-4.html">JBrowse 1.15.4 maintenance release</a></h1><p class="post-meta">October 5, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.15.4 has been released! This release allows you to use bgzip indexed FASTA, adds a new <code>categoryOrder</code> config for sorting the Hierarchical track selector, and more!
Thanks to everyone for their feature requests and bug reports, and enjoy!</p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4.zip">JBrowse-1.15.4.zip</a> - minified release</li>
<li><a href="https://github.com/GMOD/jbrowse/archive/1.15.4-release.zip">JBrowse-1.15.4-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/1.15.4-release/JBrowse-1.15.4-desktop-win32-x64.zip">JBrowse-1.15.4-desktop-win32-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-linux-x64.zip">JBrowse-1.15.4-desktop-linux-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.4-release/JBrowse-1.15.4-desktop-darwin-x64.zip">JBrowse-1.15.4-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 support for bgzipped indexed FASTA. To use, bgzip your FASTA with
<code>bgzip -i file.fa</code>, which generates file.fa.gz and file.fa.gzi and then use
<code>samtools faidx file.fa.gz</code>. If you specify the .fa.gz in the track config e.g.
<code>"urlTemplate": "file.fa.gz"</code> and have all three files in your data directory,
then they will automatically be detected (<a href="https://github.com/gmod/jbrowse/issues/1152">issue #1152</a>, <a href="https://github.com/gmod/jbrowse/pull/1200">issue #1200</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Allow fna and mfa file extensions for FASTA to be recognized by default in
the Open sequence dialog (<a href="https://github.com/gmod/jbrowse/issues/1205">issue #1205</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Improve the layout slightly for dense features (<a href="https://github.com/gmod/jbrowse/issues/1210">issue #1210</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added a <code>topLevelFeaturesPercent</code> configuration variable that can be used to
correct feature statistics estimates when <code>topLevelFeatures</code> is being used for
a track, or when it contains deeply-nested features. This configuration variable
is currently only used by BAM, BEDTabix, GFF3Tabix, and VCFTabix stores.
(<a href="https://github.com/gmod/jbrowse/issues/1147">issue #1147</a>, <a href="https://github.com/gmod/jbrowse/pull/1209">issue #1209</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Tabix-based data stores use a new storage backend based on the <code>@gmod/tabix</code> npm
module. Users should see some modest performance improvements for Tabix-based
tracks. (<a href="https://github.com/gmod/jbrowse/issues/1195">issue #1195</a>, <a href="https://github.com/gmod/jbrowse/pull/1209">issue #1209</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Added <code>hideSequenceBox</code> config to allow hiding the FASTA boxes in the View details
popups. Thanks to <a href="https://github.com/andreamini">@andreamini</a> for reporting (<a href="https://github.com/gmod/jbrowse/issues/1211">issue #1211</a>, <a href="https://github.com/gmod/jbrowse/pull/1219">issue #1219</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added <code>categoryOrder</code> config to allow sorting the categories in the Hierarchical
track selector. For example, <code>categoryOrder=VCF,Quantitative/Density,BAM</code>. Note
that we specify a lowest level subcategory e.g. Quantitative/Density to sort the
parent category Quantitative to a position (<a href="https://github.com/gmod/jbrowse/issues/1203">issue #1203</a>, <a href="https://github.com/gmod/jbrowse/pull/1208">issue #1208</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 a bug in which feature labels would sometimes be repeated across the view,
in the wrong locations. (<a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Fixed error where a chunk size limit error during histogram display would not be
displayed (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue where Open sequence dialog will open up the default "data" directory
instead of a blank instance (<a href="https://github.com/gmod/jbrowse/issues/1207">issue #1207</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Added check for PCR duplicates for CRAM features (<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue where editing the track names and types in the "Open track" dialog box
was not working when editing multiple tracks (<a href="https://github.com/gmod/jbrowse/issues/1217">issue #1217</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixed issue in which large VCF headers were not always correctly parsed by JBrowse
(<a href="https://github.com/gmod/jbrowse/issues/1139">issue #1139</a>, <a href="https://github.com/gmod/jbrowse/pull/1209">issue #1209</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Fixed issue where the histogram Y-scale bar would appear over features (issue
#1214, <a href="https://github.com/gmod/jbrowse/pull/1218">issue #1218</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/2018/08/29/jbrowse-1-15-3.html">JBrowse 1.15.3 maintenance release</a></h1><p class="post-meta">August 29, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.15.3 has been released! This contains an bugfix introduced in 1.15.0 where typing a reference sequence name in the search bar did not navigate to it properly.
It also contains a cool feature where "ultra minimal configs" can be specified by simply specifying a track label and urlTemplate</p>
<p>For example, a directory containing indexed files like VCF, BAM, GFF3 tabix, and indexed FASTA can have a config simply like this in tracks.conf</p>
<pre><code class="hljs"><span class="hljs-section">[GENERAL]</span>
<span class="hljs-attr">refSeqs</span>=volvox.fa.fai
<span class="hljs-section">[tracks.refseq]</span>
<span class="hljs-attr">urlTemplate</span>=volvox.fa
<span class="hljs-section">[tracks.bam]</span>
<span class="hljs-attr">urlTemplate</span>=volvox-sorted.bam
<span class="hljs-section">[tracks.cram]</span>
<span class="hljs-attr">urlTemplate</span>=volvox-sorted.cram
<span class="hljs-section">[tracks.vcf]</span>
<span class="hljs-attr">urlTemplate</span>=volvox.filtered.vcf.gz
<span class="hljs-section">[tracks.gff]</span>
<span class="hljs-attr">urlTemplate</span>=volvox.sort.gff3.gz
<span class="hljs-section">[tracks.bed]</span>
<span class="hljs-attr">urlTemplate</span>=volvox.sort.bed.gz
</code></pre>
<p>Enjoy browsing!</p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.3-release/JBrowse-1.15.3.zip">JBrowse-1.15.3.zip</a> - minified release</li>
<li><a href="https://github.com/GMOD/jbrowse/archive/1.15.3-release.zip">JBrowse-1.15.3-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/1.15.3-release/JBrowse-1.15.3-desktop-win32-x64.zip">JBrowse-1.15.3-desktop-win32-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.3-release/JBrowse-1.15.3-desktop-linux-x64.zip">JBrowse-1.15.3-desktop-linux-x64.zip</a></li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.3-release/JBrowse-1.15.3-desktop-darwin-x64.zip">JBrowse-1.15.3-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>Add ability to automatically deduce the storeClass and trackType of files based on
the file extension of urlTemplate. This allows very minimal configs where only
track label and urlTemplate can be specified. (<a href="https://github.com/gmod/jbrowse/pull/1189">issue #1189</a>, <a href="https://github.com/cmdcolin">@cmdcolin</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>Fixed an issue with servers that use HTTP Basic Authentication on certain browsers,
notably some Chromium, Firefox 60 and earlier, and Safari. Thanks to Keiran Raine
for reporting and <a href="https://github.com/cmdcolin">@cmdcolin</a> for debugging. (<a href="https://github.com/gmod/jbrowse/issues/1186">issue #1186</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Fix issue where searching for reference sequence names would not be navigate to the
typed in reference sequence (<a href="https://github.com/gmod/jbrowse/issues/1193">issue #1193</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/2018/08/16/jbrowse-1.15.2-maintenance-release-index.html">JBrowse 1.15.2 maintenance release</a></h1><p class="post-meta">August 16, 2018</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.15.2 has been released! This contains a couple nice features including
estimating feature density directly from the index file of BAM, VCF, and other
tabix formats. We also updated the website with a new blogging and documentation
platform! Please try it out and give us feedback.</p>
<p>Enjoy browsing!</p>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2.zip">JBrowse-1.15.2.zip</a> - 4.34 MB</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-win32-x64.zip">JBrowse-1.15.2-desktop-win32-x64.zip</a> - 69M</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-linux-x64.zip">JBrowse-1.15.2-desktop-linux-x64.zip</a> - 67M</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.15.2-release/JBrowse-1.15.2-desktop-darwin-x64.zip">JBrowse-1.15.2-desktop-darwin-x64.zip</a> - 68M</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>Created "index stats estimation" which overrides the older "global stats estimation"
that randomly samples genomic regions of BAM, VCF, etc to find feature density. This
allows initial track load to be faster automatically. (<a href="https://github.com/gmod/jbrowse/issues/1092">issue #1092</a>, <a href="https://github.com/gmod/jbrowse/pull/1167">issue #1167</a>,
<a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Removed the "full" or "dev" releases from the build. If you need a "dev" release, you
can simply download the JBrowse "source code" link from the GitHub releases page, or
use a git clone of the JBrowse repository. This will behave the same as the "dev"
release. (<a href="https://github.com/gmod/jbrowse/issues/1160">issue #1160</a>, <a href="https://github.com/gmod/jbrowse/pull/1170">issue #1170</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>JBrowse now uses a new binary-file caching and fetching backend based on the
<a href="https://www.npmjs.com/package/http-range-fetcher">http-range-fetcher</a> and
<a href="https://www.npmjs.com/package/tenacious-fetch">tenacious-fetch</a> npm modules. Users
may see slightly higher performance when viewing indexed binary formats such as BAM,
CRAM, 2bit, etc. (<a href="https://github.com/gmod/jbrowse/issues/1155">issue #1155</a>, <a href="https://github.com/gmod/jbrowse/issues/1175">issue #1175</a>, <a href="https://github.com/gmod/jbrowse/pull/1165">issue #1165</a>, <a href="https://github.com/rbuels">@rbuels</a>)</p></li>
<li><p>Updated the main jbrowse.org website to use the docusaurus platform. The main docs
for the website are now moved from the GMOD.org server to jbrowse.org. You can find
the latest documentation in the header bar. We hope you will enjoy this upgrade!
There is also a new quick start guide based on setting up JBrowse with indexed file
formats. (<a href="https://github.com/gmod/jbrowse/issues/1153">issue #1153</a>, <a href="https://github.com/gmod/jbrowse/issues/1137">issue #1137</a>, <a href="https://github.com/gmod/jbrowse/pull/1173">issue #1173</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>Added a more robust HTML processing in Util.js. Thanks to <a href="https://github.com/hkmoon">@hkmoon</a> for the idea and
implementation. (<a href="https://github.com/gmod/jbrowse/pull/1169">issue #1169</a>, <a href="https://github.com/hkmoon">@hkmoon</a>)</p></li>
<li><p>Remove utils/jb_run.js from the minified release (<a href="https://github.com/gmod/jbrowse/issues/1161">issue #1161</a>, <a href="https://github.com/gmod/jbrowse/issues/1160">issue #1160</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixes issue where navigating away from genome browser and returning would not remember
the location. Thanks to Vaneet Lotay for reporting. (<a href="https://github.com/gmod/jbrowse/issues/1168">issue #1168</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
<li><p>Fixes off-by-one in the display of the size of the genomic region being viewed. Thanks
to <a href="https://github.com/sammyjava">@sammyjava</a> for the bug report! (<a href="https://github.com/gmod/jbrowse/issues/1176">issue #1176</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</p></li>
</ul>
</span></div></article></div><div class="docs-prevnext"><a class="docs-next" href="/blog/page2/">Next →</a></div></div></div></div></div><footer class="nav-footer" id="footer"><section class="sitemap"><div><h5>Docs</h5><a href="/blog">Blog</a><a href="/docs/tutorial.html">Getting Started</a></div><div><h5>Community</h5><a href="https://gitter.im/GMOD/jbrowse">Project Chat</a><a href="https://twitter.com/JBrowseGossip" target="_blank" rel="noreferrer noopener">Twitter</a></div><div><h5>More</h5><a href="https://github.com/GMOD/jbrowse">GitHub</a><a class="github-button" href="https://github.com/GMOD/jbrowse" data-icon="octicon-star" data-count-href="/GMOD/jbrowse/stargazers" data-show-count="true" data-count-aria-label="# stargazers on GitHub" aria-label="Star this project on GitHub">Star</a></div></section><section class="copyright">Copyright © 2019 Evolutionary Software Foundation</section></footer></div></body></html>