@gmod/jbrowse
Version:
JBrowse - client-side genome browser
117 lines (113 loc) • 31.5 kB
HTML
<html lang="en"><head><meta charSet="utf-8"/><meta http-equiv="X-UA-Compatible" content="IE=edge"/><title>JBrowse 1.12.4 maintenance release · JBrowse</title><meta name="viewport" content="width=device-width"/><meta name="generator" content="Docusaurus"/><meta name="description" content="JBrowse 1.12.4 has been released, with a great many improvements and bugfixes! Apologies for the long delay since the last release."/><meta name="docsearch:language" content="en"/><meta property="og:title" content="JBrowse 1.12.4 maintenance release · JBrowse"/><meta property="og:type" content="website"/><meta property="og:url" content="https://jbrowse.org/blog/2018/02/14/jbrowse-1-12-4-maintenance-release-index.html"/><meta property="og:description" content="JBrowse 1.12.4 has been released, with a great many improvements and bugfixes! Apologies for the long delay since the last release."/><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"><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 navListItemActive"><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/2018/02/14/jbrowse-1-12-4-maintenance-release-index.html">JBrowse 1.12.4 maintenance release</a></h1><p class="post-meta">February 14, 2018</p><div class="authorBlock"></div></header><div><span><p>JBrowse 1.12.4 has been released, with a great many improvements and bugfixes! Apologies for the long delay since the last release.</p>
<p>One highlight of this release is that we have fixed a severe incompatibility that prevented many of the JBrowse formatting scripts from running correctly on Perl 5.18 and above.</p>
<p>However, there have been a HUGE number of smaller improvements and bugfixes, have a look at the release notes below!</p>
<h2><a class="anchor" aria-hidden="true" id="files-for-download"></a><a href="#files-for-download" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Files for download</h2>
<ul>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.12.4-release/JBrowse-1.12.4.zip">JBrowse-1.12.4.zip</a> - 5.7M
file SHA1 9c3b88d982ceb86de9999e49ddde631d6b41a28f</li>
<li><a href="https://github.com/GMOD/jbrowse/releases/download/1.12.4-release/JBrowse-1.12.4-dev.zip">JBrowse-1.12.4-dev.zip</a> - 30M
file SHA1 bb3fa872cbc57055712114e3e01cdcad6776a3b6</li>
</ul>
<h2><a class="anchor" aria-hidden="true" id="minor-improvements"></a><a href="#minor-improvements" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Minor improvements</h2>
<ul>
<li>Fixed SEVERE performance regression that basically made flatfile-to-json.pl
unusable on Perl 5.18 and higher. Huge thanks to Colin Diesh for tracking
this down. (<a href="https://github.com/gmod/jbrowse/issues/470">issue #470</a>, <a href="https://github.com/gmod/jbrowse/pull/912">issue #912</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Added code to calculate feature density histograms for Tabix-indexed GFF3
(<code>GFF3Tabix</code>) data sources. Thanks to <a href="https://github.com/nathandunn">@nathandunn</a> for noticing and fixing
this! (<a href="https://github.com/gmod/jbrowse/pull/956">issue #956</a>, <a href="https://github.com/nathandunn">@nathandunn</a>)</li>
<li>Added a new "Hide unspliced reads" menu item to Alignments and Alignments2
tracks that filter out reads that have no <code>N</code>s in their CIGAR strings.
Thanks to Deepak Kunni and Nathan Dunn for their work on this.
(<a href="https://github.com/gmod/jbrowse/pull/921">issue #921</a>, <a href="https://github.com/deepakunni3">@deepakunni3</a>)</li>
<li>setup.sh now uses npm instead of Bower (which is deprecated) to install
dependencies. <a href="https://github.com/enuggetry">@enuggetry</a></li>
<li>Removed legacy <code>wig-to-json.pl</code> and <code>bam-to-json.pl</code> scripts. <a href="https://github.com/rbuels">@rbuels</a></li>
<li>Added a <code>--trackConfig</code> option to <code>prepare-refseqs.pl</code> to allow injecting
refseq configuration variables at format time. (<a href="https://github.com/gmod/jbrowse/pull/884">issue #884</a>, <a href="https://github.com/erasche">@erasche</a>)</li>
<li>Added trackLabels: "no-block" config feature. Moves track labels/menus
above the features so as not to obscure the features. (<a href="https://github.com/gmod/jbrowse/issues/901">issue #901</a>, #490)</li>
<li>Added a <code>--category</code> option to <code>add-bw-track.pl</code> and <code>add-bam-track.pl</code> to
set the new track's category. Thanks to <a href="https://github.com/loraine">@loraine</a>-gueguen for the implementation!
(<a href="https://github.com/gmod/jbrowse/pull/911">issue #911</a>, <a href="https://github.com/loraine">@loraine</a>-gueguen)</li>
<li>Made jbrowse installable using <code>npm</code>. <a href="https://github.com/cmdcolin">@cmdcolin</a> and <a href="https://github.com/enuggetry">@enuggetry</a>.</li>
<li>Implemented a built-in node.js Express server <code>jb_run.js</code> for quick JBrowse launching.
<a href="https://github.com/enuggetry">@enuggetry</a></li>
<li>Added an <code>--unsorted</code> option to <code>prepare-refseqs.pl</code> that formats reference sequences
in the same order in which they appear in the input sequence file. Thanks to
<a href="https://github.com/dsenalik">@dsenalik</a> for the suggestion and implementation! (<a href="https://github.com/gmod/jbrowse/pull/924">issue #924</a>, <a href="https://github.com/dsenalik">@dsenalik</a>)</li>
<li>Allows for dot-notation instead of JSON (<a href="https://github.com/gmod/jbrowse/pull/952">issue #952</a>) for addTracks, addBookmarks,
and addStores. <a href="https://github.com/GMOD/jbrowse/pull/952">https://github.com/GMOD/jbrowse/pull/952</a>. Address security concerns
adding JSON to GET (<a href="https://nvd.nist.gov/vuln/detail/CVE-2016-6816">https://nvd.nist.gov/vuln/detail/CVE-2016-6816</a>) <a href="https://github.com/nathandunn">@nathandunn</a>.</li>
<li>If a track has no <code>key</code> set in its track configuration, JBrowse will now look for
a <code>key</code> in its track metadata, and use that if it is present. Thanks to Loraine
Guéguen for the idea (<a href="https://github.com/gmod/jbrowse/issues/957">issue #957</a>, <a href="https://github.com/gmod/jbrowse/pull/958">issue #958</a>). <a href="https://github.com/rbuels">@rbuels</a></li>
<li>Fixed bug in <code>maker2jbrowse</code> script that allows <code>maker2jbrowse</code> to be installed
in system executable directories, and adds a <code>--sortMem</code> option.
(<a href="https://github.com/gmod/jbrowse/pull/877">issue #877</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fixed a cosmetic/styling bug with malformed DOM structure in feature detail popup
dialogs. Thanks to Erik Rasche for noticing and fixing this! (<a href="https://github.com/gmod/jbrowse/pull/882">issue #882</a>, <a href="https://github.com/erasche">@erasche</a>)</li>
<li>Added a configuration option that can disable JBrowse's behavior of updating the
browser's title text as the view changes. Thanks to Luka Jeran, Primož Hadalin,
and Nathan Dunn for this! (<a href="https://github.com/gmod/jbrowse/pull/904">issue #904</a>, <a href="https://github.com/lukaw3d">@lukaw3d</a>)</li>
<li>Suppress execution of biodb-to-json.pl on sample data while running setup.sh
on MacOS High Sierra with stock Perl due to an issue with the stock Perl having
broken BerkeleyDB integration, which is needed by Bio::DB::SeqFeature::Store,
the main storage engine used by biodb-to-json.pl. Bug was manifesting as the script
running indefinitely and taking all available disk space.
(<a href="https://github.com/gmod/jbrowse/pull/945">issue #945</a>, <a href="https://github.com/gmod/jbrowse/issues/946">issue #946</a>, <a href="https://github.com/deepakunni3">@deepakunni3</a> and <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Mitigate race condition that could sometimes cause duplicate tracks to be shown
when the browser is started with the <code>loc</code> query parameeter set to the name of
a feature. Thanks to Colin Diesh for the fix. (<a href="https://github.com/gmod/jbrowse/issues/567">issue #567</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fixed issue in which JBrowse crashed when negative numbers were supplied for highlight
coordinates in the URL. Thanks to <a href="https://github.com/h2akim">@h2akim</a> for reporting, and <a href="https://github.com/cmdcolin">@cmdcolin</a> for debugging help.
(<a href="https://github.com/gmod/jbrowse/issues/769">issue #769</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Add <code>--config</code> command-line option to <code>add-bw-track.pl</code> and <code>add-bam-track.pl</code>
scripts. Thanks to Chris Childers for suggesting this! (<a href="https://github.com/gmod/jbrowse/issues/620">issue #620</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Fixed a "cannot read property 'offsetLeft'" error when using touch screens without
the old simple track selector active. (<a href="https://github.com/gmod/jbrowse/issues/893">issue #893</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Upgraded to use new Google Analytics API for usage reporting. (<a href="https://github.com/rdhayes">@rdhayes</a>)</li>
<li>Fixed bug in which start/stop codons were sometimes not displayed in the sequence
track at certain zoom levels (<a href="https://github.com/gmod/jbrowse/issues/858">issue #858</a>, pull req #859, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Fixed a regression in which the <code>defaultTracks</code> configuration variable was no longer
respected when set to a comma-separated list. (<a href="https://github.com/gmod/jbrowse/issues/892">issue #892</a>, <a href="https://github.com/gmod/jbrowse/pull/896">issue #896</a>, <a href="https://github.com/rdhayes">@rdhayes</a>)</li>
<li>Made a cosmetic change to Alignments track detail popups, changing "Length on ref" to
be displayed as "Seq length on ref", so that it is displayed more usefully next to
"Seq length". Thanks to <a href="https://github.com/colindaven">@colindaven</a> for the suggestion and implementation!
(<a href="https://github.com/gmod/jbrowse/pull/939">issue #939</a>, <a href="https://github.com/colindaven">@colindaven</a>)</li>
<li>Improved the error messages displayed when a JBrowse glyph class fails to load. Thanks
to <a href="https://github.com/scottcain">@scottcain</a> and <a href="https://github.com/cmdcolin">@cmdcolin</a> for tracking down the issue and improving the error
handling! (<a href="https://github.com/gmod/jbrowse/issues/968">issue #968</a>, <a href="https://github.com/cmdcolin">@cmdcolin</a>)</li>
<li>Added support for an <code>addFeatures</code> URL query parameter that can inject features from
the URL query string. (<a href="https://github.com/gmod/jbrowse/issues/976">issue #976</a>, <a href="https://github.com/nathandunn">@nathandunn</a>)</li>
<li>Changed the project's <code>git</code> workflow to utilize a <code>dev</code> branch that is separate from
<code>master</code>, with <code>master</code> only being updated when a new release of JBrowse is published.
(<a href="https://github.com/gmod/jbrowse/issues/975">issue #975</a>, <a href="https://github.com/enuggetry">@enuggetry</a>)</li>
<li>Implemented automated deployment of JBrowse releases to GitHub releases and <code>npm</code>.
Thanks to <a href="https://github.com/abretaud">@abretaud</a>, <a href="https://github.com/nathandunn">@nathandunn</a>, <a href="https://github.com/erasche">@erasche</a>, and <a href="https://github.com/cmdcolin">@cmdcolin</a> for valuable discussions.
(<a href="https://github.com/gmod/jbrowse/issues/822">issue #822</a>, <a href="https://github.com/gmod/jbrowse/pull/979">issue #979</a>, <a href="https://github.com/gmod/jbrowse/pull/984">issue #984</a>, <a href="https://github.com/rbuels">@rbuels</a>)</li>
<li>Added a <code>--bigwigCoverage</code> option to <code>add-bam-track.pl</code> to support configuring pregenerated
coverage histograms from the command line. Thanks to <a href="https://github.com/loraine">@loraine</a>-gueguen for the suggestion
and implementation! (<a href="https://github.com/gmod/jbrowse/pull/972">issue #972</a>, <a href="https://github.com/loraine">@loraine</a>-gueguen)</li>
<li>Improved documentation of the <code>CategoryURL</code> plugin. (<a href="https://github.com/gmod/jbrowse/pull/985">issue #985</a>, <a href="https://github.com/enuggetry">@enuggetry</a>)</li>
</ul>
</span></div></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="#files-for-download">Files for download</a></li><li><a href="#minor-improvements">Minor improvements</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>