@gmod/jbrowse
Version:
JBrowse - client-side genome browser
149 lines (145 loc) • 35.2 kB
HTML
<html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>JBrowse 1.16.0 maintenance release · JBrowse</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="I am very pleased to announce the release of JBrowse version 1.16.0!"/><meta name="docsearch:language" content="en"/><meta property="og:title" content="JBrowse 1.16.0 maintenance release · JBrowse"/><meta property="og:type" content="website"/><meta property="og:url" content="https://jbrowse.org/blog/2018/12/13/jbrowse-1-16-0.html"/><meta property="og:description" content="I am very pleased to announce the release of JBrowse version 1.16.0!"/><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="sideNavVisible separateOnPageNav"><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"><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 navListItemActive"><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>
document.addEventListener('DOMContentLoaded', function() {
createToggler('#navToggler', '#docsNav', 'docsSliderActive');
createToggler('#tocToggler', 'body', 'tocActive');
const headings = document.querySelector('.toc-headings');
headings && headings.addEventListener('click', function(event) {
if (event.target.tagName === 'A') {
document.body.classList.remove('tocActive');
}
}, false);
function createToggler(togglerSelector, targetSelector, className) {
var toggler = document.querySelector(togglerSelector);
var target = document.querySelector(targetSelector);
toggler.onclick = function(event) {
event.preventDefault();
target.classList.toggle(className);
};
}
});
</script></nav></div><div class="container mainContainer postContainer blogContainer"><div class="wrapper"><div class="lonePost"><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><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></div><div class="blogSocialSection"></div></div><div class="blog-recent"><a class="button" href="/blog">Recent Posts</a></div></div></div><nav class="onPageNav"><ul class="toc-headings"><li><a href="#major-improvements">Major improvements</a></li><li><a href="#minor-improvements">Minor improvements</a></li><li><a href="#bug-fixes">Bug fixes</a></li><li><a href="#notable-changes">Notable changes</a></li></ul></nav></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>