@gmod/jbrowse

<!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> 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="posts"><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/11/28/jbrowse-1-7-3-bugfix-release-index.html">JBrowse 1.7.3 bugfix release</a></h1><p class="post-meta">November 28, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.7.3 has been released, containing fixes for some more issues found in the <a href="http://jbrowse.org/jbrowse-1-7-2-bugfix-release/" title="JBrowse 1.7.2 bugfix release">1.7.2 release</a> and earlier. Remote BAM access is rather difficult to get right, thanks very much to the people who continue to step forward to report and help correct problems with JBrowse displaying their BAM data.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=31" title="download JBrowse-1.7.3.zip">JBrowse-1.7.3.zip</a> - 2.9M</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=32" title="download JBrowse-1.7.3-dev.zip">JBrowse-1.7.3-dev.zip</a> - 28.6M Changes in this release:</p></li> <li><p>Fixed several more bugs in the BAM data backend that prevented display of some BAM files. Thanks to Gleb Kuznetzov for help in isolating these.</p></li> <li><p>Fixed bug in display of faceted track selector in which the facet titles were taking up too much vertical height. Thanks to Steffi Geisen for pointing this out.</p></li> <li><p>"Alignments" tracks now parse an alignment's CIGAR string if it does not have an MD field, and display mismatches and skipped sequence regions (particularly important for RNA-seq alignments). Thanks to Gregg Helt for providing the sample dataset used to test this.</p></li> <li><p>Added support for a <code>showReverseStrand</code> config variable to Sequence track that, if set to false, turns off display of the reverse sequence strand.</p></li> <li><p>"Alignments" tracks now show reads with missing mate pairs with a red crosshatched pattern instead of with a red border.</p></li> <li><p>Added an Apache .htaccess file to the JBrowse root directory that enabled CORS by default for all files under it, if AllowOverride is on.</p></li> <li><p>Fixed bug in which the vertical scroll position can sometimes be set too far down when zooming in and out.</p></li> <li><p>Fixed some bugs in server-side formatting code for feature tracks: data was recorded multiple times in JSON files in some circumstances. Thanks to Volodymyr Zavidovych and Steffi Geisen for pointing this out.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/11/09/jbrowse-1-7-2-bugfix-release-index.html">JBrowse 1.7.2 bugfix release</a></h1><p class="post-meta">November 9, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.7.2 has been released, containing a fix for some further BAM issues found in the <a href="http://jbrowse.org/jbrowse-1-7-1-bugfix-release/" title="JBrowse 1.7.1 bugfix release">1.7.1 release</a>. Thanks so much to everyone who has worked with me to isolate problems in JBrowse's BAM support. The more people report problems, the more bulletproof the BAM backend gets.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=29" title="download JBrowse-1.7.2.zip">JBrowse-1.7.2.zip</a> - 2.9M</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=30" title="download JBrowse-1.7.2-dev.zip">JBrowse-1.7.2-dev.zip</a> - 28.6M Changes in this release:</p></li> <li><p>Fixed more bugs in BAM backend that failed to load some BAM files, including BAM files containing no alignments. Thanks to John St. John for his assistance in isolating the problem.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/11/07/jbrowse-1-7-1-bugfix-release-index.html">JBrowse 1.7.1 bugfix release</a></h1><p class="post-meta">November 7, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.7.1 has been released, containing fixes for some issues in the <a href="http://jbrowse.org/jbrowse-1-7-0/" title="JBrowse 1.7.0, now with data export, direct BAM display, and much more">1.7.0 release</a>.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=27" title="download JBrowse-1.7.1.zip">JBrowse-1.7.1.zip</a> - 2.9M</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=28" title="download JBrowse-1.7.1-dev.zip">JBrowse-1.7.1-dev.zip</a> - 28.3M Changes in this release:</p></li> <li><p>Fixed bug in which bars below the origin of <code>Wiggle/XYPlot</code> were drawn incorrectly (issue #161). Thanks to GitHub user @makela for pointing this out.</p></li> <li><p><code>Wiggle/XYPlot</code> tracks now by default draw a horizontal line at the origin, and support a <code>style.origin_color</code> configuration variable to set its color or turn it off.</p></li> <li><p>Fixed bug in BAM backend that caused an infinite loop and/or browser crash with some BAM files. Thanks to Gleb Kuznetzov for pointing this out.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a 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></h1><p class="post-meta">November 5, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I am pleased to announce the release of JBrowse 1.7.0, which includes a great many enhancements both large and small. Very exciting!</p> <p>First, the download links:</p> <ul> <li><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=25" title="download JBrowse-1.7.0.zip">JBrowse-1.7.0.zip</a> - 2.9M - Includes everything you need to display your data on the web with JBrowse, optimized for loading speed.</li> <li><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=26" title="download JBrowse-1.7.0-dev.zip">JBrowse-1.7.0-dev.zip</a> - 27.4M - Primarily for developers. Includes additional developer documentation, developer tests suites, and full copies of Dojo and Dijit. Now for the big new features.</li> </ul> <p>Firstly, JBrowse can now <strong>quickly and efficiently display alignment data directly from BAM files</strong> over the web, with no need for any intermediate formatting steps. Just put your <code>.bam</code> and <code>.bai</code> files on your web server, add a few lines of configuration to point JBrowse at them, and go! Moreover, JBrowse has <strong>two new track types optimized for displaying alignment data</strong>: new** "Alignments" track type**, showing basepair differences and insertions between aligned reads and the reference (using a BAM alignment's MD field), and a new <strong>FeatureCoverage</strong> track type that generates a <strong>depth-of-coverage plot from a BAM file</strong> (or from any other source of feature data). Many thanks to Thomas Down and his Dalliance Genome Browser project, from which the JBrowse BAM data backend was derived.</p> <p>The second headline feature of this release is long-awaited support for <strong>exporting and <strong><span style="color: #000000;"></strong>saving sequence and annotation data</strong> in FASTA, GFF3, bed, bedGraph, and Wiggle formats. Just turn on the track of interest and click on its track label to bring up a new menu of things you can do with that track, one of which is "Save track data". This has been one of the top features users have been requesting for a long time, and now it's finally here!</span></p> <p>Third, we have two important enhancements to JBrowse's already-excellent support for <strong>BigWig**** quantitative data</strong>: a new <strong>Wiggle/Density</strong> track type, analogous to GBrowse's popular <code>wiggle_density</code> track type, that shows quantitative data using varying intensity of color. Additionally, the existing <strong>Wiggle/XYPlot</strong> supports a new <code>bg_color</code> option that, if set, provides a background color for all data points in the track, making it easy to <strong>distinguish between regions with no data, and regions with 0-valued data</strong>. Many thanks to Steffi Geisen at the University of Granada for her continued help driving progress on this and many other issues.</p> <p>Read on for the exhaustive list of changes in this release, including bug fixes, more keyboard navigation enhancements, colored DNA basepairs, more configuration options, and speed enhancements.</p> <p>1.7.0 2012-11-05 19:22:17 America/New_York</p> <ul> <li><p>Added a new direct-access storage driver for BAM files, removing the need for <code>bam-to-json.pl</code>. This new method of BAM access is far superior to the old <code>bam-to-json.pl</code> in nearly every way, except in browser compatibility. Like the BigWig direct access backend added in JBrowse 1.5.0, it is based on code from Thomas Down's Dalliance Genome Explorer, and works in all major browsers <em>except</em> Internet Explorer, because IE lacks support for the necessary web standards. It may work with Internet Explorer 10, but this has not been tested yet.</p></li> <li><p>Added a new <code>Alignments</code> track type designed to work seamlessly with BAM files. This track type shows basepair differences and insertions between aligned reads and the reference, and highlights reads with missing mate-pairs in red.</p></li> <li><p>Added the ability to export track data in FASTA, GFF3, bed, bedGraph, and Wiggle formats (issue #104). To export data, turn on the track of interest, then click on its track label to bring up the track menu, and select "Save track data".</p></li> <li><p>Added a new <code>Wiggle/Density</code> track type, analagous to the GBrowse <code>wiggle_density</code> glyph type. Shows the Wiggle information using varying intensity of color (issue #66). Renamed the <code>Wiggle</code> track to <code>Wiggle/XYPlot</code>, and made the old <code>Wiggle</code> track type an alias to <code>Wiggle/XYPlot</code>.</p></li> <li><p>Both <code>Wiggle/XYPlot</code> and <code>Wiggle/Density</code> now support a <code>style -> bg_color</code> option. Color-density plots blend the <code>pos_color</code> or <code>neg_color</code> into the <code>bg_color</code> in amounts that vary with the wiggle data, and xyplots fill the background color behind all points that have data present, regardless of value. <code>bg_color</code> defaults to off for xy xplots, and semi-transparent gray for density plots. Setting this makes it easier for users to distinguish at a glance between regions with no data, and regions with a value of 0.</p></li> <li><p>Added a new <code>FeatureCoverage</code> track type, which shows a dynamically-computed XY-plot of the depth of coverage of features across a genome. One good use of this track type is to provide a quick coverage plot directly from a BAM file. However, since this track calculates coverage on the fly, it can be slow when used with large regions or very deep coverage. In this case, it is recommended to generate a BigWig file containing the coverage data, and display it with a <code>Wiggle/XYPlot</code> or <code>Wiggle/Density</code> track.</p></li> <li><p>DNA bases are now displayed with color-coded backgrounds, allowing basepair information to be discerned when zoomed somewhat further out, when base letter cannot be drawn. Colors are also designed to match the base-mismatch colors used in <code>Alignment</code> tracks, enabling clearer SNP visualization.</p></li> <li><p>Added a vertical line cursor and labels showing the current basepair position of the mouse when hovering over the scale bar, or when doing a rubber-band zoom (Erik Derohanian) (issue #32).</p></li> <li><p>Added an animation to make it easier to see where in the track selection list a closed track has gone, when using the simple track selector (issue #151).</p></li> <li><p>Information dialog boxes are now easier to dismiss: clicking anywhere outside of them, or pressing any key, will make them go away.</p></li> <li><p>Improvements to feature track configuration:</p> <ul> <li>Feature tracks no longer use the <code>style.subfeatureScale</code> configuration variable to determine whether to show subfeatures. Instead, subfeatures are shown if the parent feature, when shown on the screen, is wider than <code>style.minSubfeatureWidth</code>, which defaults to 6 pixels.</li> <li>Make explicitly-configured track <code>labelScale</code>, <code>histScale</code>, and <code>descriptionScale</code> not be modulated by the feature density: only use the feature density to pick the scale defaults</li> </ul></li> <li><p>The default feature-detail dialog box now shows more information, adding:</p> <ul> <li>the feature's exact length</li> <li>full details of its subfeatures</li> </ul></li> <li><p>Added a <code>locationBoxLength</code> configuration variable that controls the width of the location box. In addition, the default width of the location box is now also smarter. Instead of a fixed 25 characters, it is calculated to fit the largest location string that is likely to be produced, based on the length of the reference sequences and the length of their names.</p></li> <li><p>Pressing SHIFT+-up/down arrow keys now cause the genome view to zoom in and out. If ALT is added, it zooms further. Thanks to Karsten Hokamp for the excellent suggestion.</p></li> <li><p>Holding SHIFT while scrolling left and right with the arrow keys causes the view to scroll further.</p></li> <li><p>Added a <code>theme</code> configuration variable to allow changing the graphical theme to something different from the default "tundra". However, no other themes are implemented yet.</p></li> <li><p>Greatly sped up rendering of HTML subfeatures by caching the heights of subfeature HTML elements.</p></li> <li><p>Fixed bug in which the genome view executed a double-click zoom when users rapidly clicked on multiple track 'close' buttons.</p></li> <li><p>Fixed bug with the genome view scrolling in response to arrow keys being pressed when typing in the location box.</p></li> <li><p>Fixed bug in which the score display in Wiggle tracks would sometimes flicker when moving the mouse.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/10/26/jbrowse-1-6-5-bugfix-release-index.html">JBrowse 1.6.5 bugfix release</a></h1><p class="post-meta">October 26, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I'm pleased to announce the release of JBrowse 1.6.5, containing some small new features, plus fixes for some issues in the <a href="http://jbrowse.org/jbrowse-1-6-4-bugfix-release/" title="JBrowse 1.6.4 bugfix is also coming along very soon, with a (we hope!) very impressive set of new features. Stay tuned.release">1.6.4 release</a>.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=23" title="download JBrowse-1.6.5-min.zip">JBrowse-1.6.5-min.zip</a> - 2.8M</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=24" title="download JBrowse-1.6.5-full.zip">JBrowse-1.6.5-full.zip</a> - 27.3M Changes in this release:</p></li> <li><p>The location box now shows the <strong>length of the currently visible</strong> ** region** in parentheses. For example: <code>ctgB:1244..3566 (2.32 Kb)</code>. Thanks to Karsten Hokamp for the suggestion!</p></li> <li><p>The <strong>arrow keys</strong> on the keyboard can now be used to pan and scroll around the genome view.</p></li> <li><p>Wiggle track mouseover cursors now display the score with only 6 significant digits, avoiding confusion over approximations introduced by scores being converted to IEEE floating-point numbers (as for BigWig files) and back to text.</p></li> <li><p>The faceted track selector now renders any HTML that may be present in the track metadata by default. To turn this off, it now accepts an <code>escapeHTMLInData</code> option that, if set to <code>true</code> or <code>1</code>, will not render the HTML, but will instead display the raw code (issue #145).</p></li> <li><p>Upgraded to a more recent version of jszlib, which contains some important bugfixes (issue #157).</p></li> <li><p>Fixed bug dealing with very large regions with the same value in canvas-based Wiggle tracks (also issue #157).</p></li> <li><p><code>prepare-refseqs.pl</code> now by default uses a <strong>more scalable directory</strong> ** structure for storing sequences**. This fixes problems some users were experiencing with large numbers of reference sequences (issue #139).</p></li> <li><p><code>ucsc-to-json.pl</code> now supports a <code>--primaryName</code> option allowing the users to <strong>alter which UCSC data field is displayed by JBrowse as</strong> ** the primary name** of the features in a track. Also, <code>ucsc-to-json.pl</code> now treats as indexable names all UCSC data columns called "name", "alias", or "id" followed by zero or more digits. Thanks to Steffi Geisen for this suggestion.</p></li> <li><p>Fixed "Duplicate specification" warnings coming from <code>flatfile-to-json.pl</code> and <code>remove-track.pl</code>.</p></li> <li><p>Fixed bugs in which both the first few and the last few bases of a reference sequence were not displaying correctly in a DNA track.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/10/16/jbrowse-1-6-4-bugfix-release-index.html">JBrowse 1.6.4 bugfix release</a></h1><p class="post-meta">October 16, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.6.4 has been released, containing fixes for some small issues in the <a href="http://jbrowse.org/jbrowse-1-6-3-bugfix-release/" title="JBrowse 1.6.3 bugfix release">1.6.3 release</a>.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=21" title="download JBrowse-1.6.4-min.zip">JBrowse-1.6.4-min.zip</a> - 2.8M</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=22" title="download JBrowse-1.6.4-full.zip">JBrowse-1.6.4-full.zip</a> - 27.3M Changes in this release:</p></li> <li><p>Improvements to the scalability of <code>generate-names.pl</code>. Many thanks to Steffi Geisen for her ongoing help with this.</p> <ul> <li>Users can now manually specify which tracks will be indexed to enable autocompletion and searching for their feature names in the JBrowse location box.</li> <li>The lazy-trie name indexing structure now correctly handles the case of large numbers of features that may share the same name. Before, it was generating files that were too large for the client to handle.</li> </ul></li> <li><p>Fixed off-by-one error in Wiggle track display code: wiggle data was incorrectly displayed shifted one base to the left of its proper position. Thanks to Steffi Geisen for noticing this.</p></li> <li><p>Fixed bug in which the reference-sequence selection box did not automatically update in all situations to reflect the current reference sequence.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/09/28/jbrowse-1-6-3-bugfix-release-index.html">JBrowse 1.6.3 bugfix release</a></h1><p class="post-meta">September 28, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.6.3 has been released, containing fixes for some small issues in the <a href="http://jbrowse.org/jbrowse-1-6-2-bugfix-release/" title="JBrowse 1.6.2 bugfix release">1.6.2 release</a>.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=19" title="download JBrowse-1.6.3-min.zip">JBrowse-1.6.3-min.zip</a> - 2.8M</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=20" title="download JBrowse-1.6.3-full.zip">JBrowse-1.6.3-full.zip</a> - 27.3M Changes in this release:</p></li> <li><p>Fixed bug with shift-rubberband-zooming not working on Windows (issue #150) (Erik Derohanian).</p></li> <li><p>Fixed "Can't locate JSON.pm" errors with add-track-json.pl.</p></li> <li><p>Added a reference-sequence-selection dropdown box, similar to the old one, that is shown by default if fewer than 30 reference sequences, otherwise it's off unless <code>refSeqDropdown: true</code> is set in the configuration (issue #138).</p></li> <li><p>Fixed bug in which popup dialog boxes showing other websites showed the website in only the top portion of the dialog box. Only present in some browsers (issue #149).</p></li> <li><p>Fix coordinate display bug in feature detail popups. The feature's position was being displayed in interbase coordinates, but should be displayed in 1-based coordinates. Thanks to Steffi Geisen for pointing this out.</p></li> <li><p>Added a <code>style.height</code> option to Wiggle tracks to control the track's height in pixels (issue #131) (Erik Derohanian).</p></li> <li><p>Added support for a <code>style.trackLabelCss</code> configuration variable to allow customizing the appearance of the label for a particular track (issue #4) (Erik Derohanian).</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/09/10/jbrowse-1-6-2-bugfix-release-index.html">JBrowse 1.6.2 bugfix release</a></h1><p class="post-meta">September 10, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.6.2 has been released, containing fixes for some small issues in the <a href="http://jbrowse.org/jbrowse-1-6-1-bugfix-release/" title="JBrowse 1.6.1 bugfix release">1.6.1 release</a>.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=18" title="download JBrowse-1.6.2-min.zip">JBrowse-1.6.2-min.zip</a> - 2.8M</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=17" title="download JBrowse-1.6.2-full.zip">JBrowse-1.6.2-full.zip</a> - 27.3M Changes in this release:</p></li> <li><p>Fixed feature-layout performance problem when zoomed very far in on features that are much larger than the viewing window.</p></li> <li><p>Added a default <code>menuTemplate</code> to all HTML-based features, so that all HTML features now have a right-click menu by default.</p></li> <li><p>Add <code>css</code> configuration variable that allows users to specify either strings or URLs containing CSS to add.</p></li> <li><p>improved <code>bin/ucsc-to-json.pl</code> error messages</p></li> <li><p><code>bin/add-track-json.pl</code> now replaces tracks in the target configuration if they have the same label.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a 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></h1><p class="post-meta">September 7, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>I had the great honor of being invited to the [BioHackathon 2012](BioHackathon 2012), held this past week in Toyama, Japan and funded by Japan's National Bioscience Database Center (<a href="http://biosciencedbc.jp/?lng=en">NBDC</a>) and Database Center for Life Science (<a href="http://dbcls.rois.ac.jp/en/">DBCLS</a>). It's been an exhausting week of immersing myself in Semantic Web technologies: RDF, <a href="http://www.w3.org/TR/sparql11-query/">SPARQL</a>, <a href="http://sadiframework.org">SADI</a>, and lots and lots of ontologies. A lot of work still needs to be done, but there really are revolutionary capabilities coming to bioinformatics from this direction.</p> <p>At the hackathon, I worked on a SPARQL-based data backend for JBrowse, which will be released as part of the upcoming JBrowse 1.7.0. It is shaping up to be surprisingly fluid, especially given the less-than-speedy reputation of today's triple stores.</p> <p>Until it is merged into master, work on the JBrowse triple store can be seen at <a href="https://github.com/GMOD/jbrowse/compare/master...triplestore">https://github.com/GMOD/jbrowse/compare/master...triplestore</a></p> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2012/08/28/jbrowse-1-6-1-bugfix-release-index.html">JBrowse 1.6.1 bugfix release</a></h1><p class="post-meta">August 28, 2012</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.6.1 has been released, containing fixes for some small issues in the <a href="http://jbrowse.org/jbrowse-1-6-0-released-includes-feature-descriptions-and-more/" title="JBrowse 1.6.0 released, includes feature descriptions and more!">1.6.0 release</a>.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=16" title="download JBrowse-1.6.1-min.zip">JBrowse-1.6.1-min.zip</a> - 2.8M</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=15" title="download JBrowse-1.6.1-full.zip">JBrowse-1.6.1-full.zip</a> - 27.3M Changes in this release:</p></li> <li><p>JBrowse now attempts to prevent feature labels being obscured by track labels by keeping the feature labels a bit further away from the left side of the view, if possible.</p></li> <li><p>Fixed bug in which welcome page was not shown when JBrowse has not been configured yet (issue #130).</p></li> <li><p>Fixed bug in which passing <code>tracklist=0</code> (as when running the browser in embedded mode) caused JBrowse to crash (issue #132).</p></li> <li><p>Added dependency on Bio::GFF3::LowLevel::Parser 1.4, which has an important bugfix related to multi-location features (issue #109).</p></li> </ul> </span></div></article></div><div class="docs-prevnext"><a class="docs-prev" href="/blog/page6/">← Prev</a><a class="docs-next" href="/blog/page8/">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>