@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/2013/09/23/jbrowse-1-10-4-index.html">JBrowse 1.10.4 maintenance release</a></h1><p class="post-meta">September 23, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.10.4 has been released, with a new simple sequence-search track tool, large performance improvements for <code>generate-names.pl</code>, and some new filtering options for VCF-based variant tracks.</p> <p>Files for download:</p> <ul> <li><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=69" title="download JBrowse-1.10.4.zip">JBrowse-1.10.4.zip</a> - 4.6M file SHA1 0cfc8106e0b89fcc937701be74830c30b9f894cc</li> <li><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=70" title="download JBrowse-1.10.4-dev.zip">JBrowse-1.10.4-dev.zip</a> - 26M file SHA1 9b4d7aa9c6cb702853e3080fd7dedfae32a095ca</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>Rewrote many parts of generate-names.pl, making heavy use of temporary BerkeleyDB stores (using Perl's DB_File module). This improves generate-names.pl performance by more than 10x.</li> <li>Added a File->Add sequence search track menu item that can make tracks that show which regions of the reference sequence contain a given (small) sequence, or match a given regular expression. Thanks to Daniel Kasenberg for the initial implementation of this (issue #315).</li> <li>Added a CanvasVariants track type, similar to HTMLVariants, which utilizes the faster CanvasFeatures rendering backend for displaying variant data.</li> <li>Added checkboxes to HTMLVariants and CanvasVariants track menus that allow filtering displayed features based on the FILTER attribute in a VCF file. In addition to filtering based on the presence or absence of PASS, users can filter based on the custom filters defined in the VCF header. Thanks to Keiran Raine and Andrew Uzilov for suggesting this (issue #344).</li> <li>Added "Hide forward strand" and "Hide reverse strand" checkboxes to Alignments and Alignments2 track menus that allow alignments on the forward and/or reverse strands to be hidden.</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>Fixed a bug that prevented indexing of feature aliases in the names index when running generate-names.pl.</li> <li>Fixed a bug that prevented proper display of the "ibeam" feature class in HTMLFeatures tracks. Thanks to Ed Lee for pointing this out.</li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/09/04/jbrowse-1-10-3-index.html">JBrowse 1.10.3 maintenance release</a></h1><p class="post-meta">September 4, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.10.3 has been released, with a lot of small enhancements and important bugfixes.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=67" title="download JBrowse-1.10.3.zip">JBrowse-1.10.3.zip</a> - 4.8M file SHA1 3be482df63ce10a9211483bc760d3b4137a2e77f</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=68" title="download JBrowse-1.10.3-dev.zip">JBrowse-1.10.3-dev.zip</a> - 26M file SHA1 825093524bbf09f0f724f80332342b99f8e50734 <span style="color: #000000; font-size: 1.8em; line-height: 1.5em;">Minor improvements</span></p></li> <li><p>Added options to Alignments, Alignments2, and SNPCoverage tracks to allow hiding reads that are duplicates, fail vendor QC, have missing mate pairs, are secondary alignments, and/or are supplementary alignments. Thanks to Kieran Raine and Andrew Uzilov for pointing out the need for this, and for their input on its design (issue #332).</p></li> <li><p>Added support for a <code>variables</code> configuration for SPARQL data stores that can be used to specify additional variables for interpolating into a SPARQL query. Thanks to Toshiaki Katayama for suggesting this.</p></li> <li><p>Added the ability for Sequence tracks to display a 6- or 3-frame translation of the reference sequence. Thanks to Daniel Kasenberg for implementing this (issue #221).</p></li> <li><p>Added checkboxes in the track menu of Sequence tracks that allow users to toggle the display of the forward strand, reverse strand, and 6-frame translation.</p></li> <li><p>Added support for an <code>addStores</code> variable in the query string of the URL used to start JBrowse. This variable accepts store configurations (which are a way to specify data sources separately from track configurations, so multiple tracks can use the same data source) in JSON format. For example, to add a store called "urlbam" that points to a BAM file, you could use the JSON:<code>{ "urlbam": { "type": "JBrowse/Store/SeqFeature/BAM", "urlTemplate": "/path/to/my/bamfile.bam" }}</code></p></li> </ul> <p>which, when URI-escaped and put in the query string, looks like:</p> <p><code>addStores=%7B%20%22urlbam%22%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FBAM%22%2C%20%22urlTemplate%22%3A%20%22%2Fpath%2Fto%2Fmy%2Fbamfile.bam%22%20%7D%7D</code></p> <ul> <li>Slightly improved performance of generate-names.pl in cases where --completionLimit is zero. Also improved the POD documentation of the --completionLimit parameter for generate-names.pl. Thanks to Richard Hayes for his continued patience.</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>Fixed some bugs that prevented proper display of BigWig files larger than 4GB. Thanks to Keiran Raine for pointing this out.</li> <li>Fixed a major performance bug that unnecessarily slowed down display of large BigWig files with Wiggle tracks when <code>autoscale</code> is set to "local".</li> <li>Fixed a bug that prevented display of BAM reads that had MD tags but no associated CIGAR string. Thanks to Keiran Raine for point this out (issue #330).</li> <li>Fixed a bug in which FixedImage tracks (e.g. legacy image-based Wiggle tracks) never take down the "Loading" message when displaying on a reference sequence for which no image data has been provided.</li> <li>Fixed a bug that prevented rendering of mismatches, insertions, and deletions in a BAM read that occurred after a skip. Thanks to Gregg Helt for noticing this and fixing it (issue #325).</li> <li>Fixed a bug in which the SNP frequencies calculated by SNPCoverage tracks were sometimes incorrect. Thanks to Matthew Conte for pointing this out (issue #335).</li> <li>Fixed a bug in which reference sequences with a start coordinate other than zero would cause the overview scale track to not be drawn correctly. Thanks to Gregg Helt for noticing this and working on an initial fix (issue #324).</li> <li>Fixed a bug in which the most recent location visited on a given reference sequence was not properly being restored from the saved cookie. Thanks to Gregg Helt for the initial fix for this (issue #321).</li> <li>Fixed a bug in which event handlers and blocks in CanvasFeatures tracks were not being properly cleaned up. The most prominent visible consequences of this were duplicate dialog boxes being opened when clicking on a canvas feature. Thanks to Keiran Raine for noticing this and making sure it was fixed (issue #329).</li> <li>Fixed a bug with flatfile-to-json.pl parsing of GenBank locations. Thanks to Steve Marshall for pointing this out (issue #323).</li> <li>Fixed a bug in which SNPCoverage tracks would not always properly display error messages when something goes wrong, particularly under IE 9.</li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/08/15/jbrowse-1-10-2-index.html">JBrowse 1.10.2 maintenance release</a></h1><p class="post-meta">August 15, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.10.2 has been released, with fixes for some minor issues, and some minor improvements to the CanvasFeatures track.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=65" title="download JBrowse-1.10.2.zip">JBrowse-1.10.2.zip</a> - 5.2M file SHA1 4e00586e070d8797a3598b405d3502906993c4e5</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=66" title="download JBrowse-1.10.2-dev.zip">JBrowse-1.10.2-dev.zip</a> - 26M file SHA1 8865724542fcbdec5de974273b27e0a10680156b Changes in this release:</p></li> <li><p>Added mouse-over 'tooltips' to to CanvasFeatures tracks that show the a feature's label and description when the mouse hovers over it. Thanks to Daniel Kasenberg for implementing this.</p></li> <li><p>Strand arrowheads in CanvasFeatures tracks now attempt to stay visible on the screen, like they do in HTMLFeatures tracks. Thanks to Daniel Kasenberg for implementing this.</p></li> <li><p>Fixed bugs and inefficiencies preventing JBrowse from handling very dense BigWig files. Thanks to Michael Axtell for pointing this out (issue #312).</p></li> <li><p>Fixed a bug in which features were not always laid out correctly in CanvasFeature tracks when the display mode is set to "compact".</p></li> <li><p>Fixed a bug causing the text labels of mismatching bases in Alignments2 tracks (i.e. <code>Alignments</code> canvas glyphs) to be slightly misaligned vertically when feature labels are turned on (they are off by default for Alignments glyphs).</p></li> <li><p>Fixed a bug preventing the <code>defaultTracks</code> configuration variable from operating correctly.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/08/06/jbrowse-1-10-1-maintenance-release-index.html">JBrowse 1.10.1 maintenance release</a></h1><p class="post-meta">August 6, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.10.1 has been released, with fixes for some minor issues and one major issue.</p> <p>Files for download:</p> <ul> <li><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=63" title="download JBrowse-1.10.1.zip">JBrowse-1.10.1.zip</a> - 5.2M file SHA1 3677d10ba4ffd6ba604871dc11b1989131baff9f</li> <li><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=64" title="download JBrowse-1.10.1-dev.zip">JBrowse-1.10.1-dev.zip</a> - 26M file SHA1 f6a1a89d42498887ee0123ce2b98afea4478b6e0</li> </ul> <p>Changes in this release:</p> <ul> <li><p>Added support in <code>maker2jbrowse</code> for user-defined source tags in GFF3 output from MAKER. Thanks to Carson Holt for contributing this fix.</p></li> <li><p>NCList data stores (actually the array representation used therein) now store feature attribute names case-insensitively.</p></li> <li><p>Fixed a bug in which features in canvas-based feature tracks could not be clicked in Firefox. Thanks to GitHub user mke21 for pointing this out, and to Daniel Kasenberg for fixing my fix to work with older versions of Chrome.</p></li> <li><p>Fixed a bug with client-side GFF3 parsing in which the strand of features was not being correctly parsed.</p></li> <li><p>Fixed bug preventing backward-compatibility with 1.2.1-formatted data. Thanks to Daniel Kasenberg for implementing this.</p></li> <li><p>Fixed a bug in the Gene glyph that caused the browser to crash if a gene feature has no subfeatures.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a 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></h1><p class="post-meta">July 30, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>After a long, hard development push, JBrowse 1.10.0 is out today! There are several major improvements in this release, and a <strong>huge</strong> number of smaller improvements and bugfixes.</p> <h3><a class="anchor" aria-hidden="true" id="download-links"></a><a href="#download-links" 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>Download links</h3> <ul> <li><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=61" title="download JBrowse-1.10.0.zip">JBrowse-1.10.0.zip</a> - 5.2M - Includes everything you need to display your data on the web with JBrowse, optimized for fast loading speed.</li> </ul> <div>SHA1 file checksum: 8dddbcbc54d5be967b1d381cb6ad8ace671536e7</div> * [JBrowse-1.10.0-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=62 "download JBrowse-1.10.0-dev.zip") - 26M - Primarily for developers. Includes additional developer documentation, developer test suites, and full copies of Dojo, Dijit, and DojoX. <div>SHA1 file checksum: 8856e1301d90df93ba4a644bccc48c3b4d6dc07c</div> <h2><a class="anchor" aria-hidden="true" id="major-new-features"></a><a href="#major-new-features" 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 new features</h2> <ul> <li><p>Added powerful <strong>combination tracks</strong>, which can combine data from multiple other tracks using <strong>range, arithmetic, or masking</strong> ** operations**. For example, a BigWig track can be masked to highlight only regions that lie within features from a BAM track. Or the intersection of two or more feature tracks can be calculated. To create a combination track, select "File->Add combination track" from the menu bar, and then add tracks to the new combination track by dragging them into it. A huge thanks to OICR co-op students Julien Smith-Roberge and Daniel Kasenberg for implementing this powerful feature. It's a very significant accomplishment!</p></li> <li><p>Added** "normal", "compact", and "collapsed" feature layout options** for canvas-based feature tracks (currently just Alignments2 tracks). Thanks to OICR co-op student Daniel Kasenberg for implementing this!</p></li> <li><p>Greatly improved the** <code>JBrowse/View/Track/CanvasFeatures</code> track** ** type, to the point where it is probably ready for experienced** ** JBrowse users to use** in earnest. It renders features using a modular glyph system that GBrowse users will find very familiar. To give it a try, simply change the <code>type</code> key in an existing track configuration to "JBrowse/View/Track/CanvasFeatures" and add a <code>glyph</code> key to set which glyph to use. Glyphs that are currently implemented are:</p> <ul> <li>Box - draws a box, optionally with an arrow indicating strandedness.</li> <li>Segments - draws a series of boxes connected with a line, for features with subparts.</li> <li>ProcessedTranscript - draws CDS and UTR features, with UTRs a different color and thinner.</li> <li>Gene - draws a group of aligned ProcessedTranscript glyphs for mRNAs that are subfeatures of a top-level gene feature. Each of these glyphs have been patterned as near-clones of the (very popular) analogous glyphs in GBrowse.</li> </ul></li> <li><p>Added a <strong>SPARQL data backend</strong> to allow displaying features directly from a SPARQL endpoint. Many thanks to the NDBC/DBCLS BioHackathon 2012 and 2013 participants for suggesting this and helping with this work! See <a href="http://www.biohackathon.org">http://www.biohackathon.org</a> for more on this fantastic (and I think very important) series of hackathons.</p></li> <li><p>There is a new "Highlight" button next to the "Go" button that lets a user quickly and easily highlight a region with the mouse.</p></li> <li><p>Added the ability to** "pin" some tracks to the top of the display**,</p></li> <li><p>so that they stay at the top of the pane while the rest of the tracks are scrolled vertically. Thanks to the WebApollo project for suggesting this.</p></li> <li><p>Integrated a** <code>maker2jbrowse</code> script** into the core JBrowse distribution. You can now visualize your MAKER results in JBrowse with a single command: <code>bin/maker2jbrowse -d /path/to/your/maker/master_datastore_index.log</code> Thanks to the MAKER team and Yandell lab for providing the initial implementation of <code>maker2jbrowse</code>.</p></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>Added support for an <code>addFeatures</code> variable in the query string of the URL used to start JBrowse. This variable accepts feature data in JSON format in the form:<code>[{ "seq_id":"ctgA", "start": 123, "end": 456, "name": "MyBLASTHit"},...}]</code>which, when URI-escaped and put in the query string, looks like:<code>addFeatures=%5B%7B%20%22seq_id%22%3A%22ctgA%22%2C%20%22start%22%3A%20123%2C%20%22end%22%3A%20456%2C%20%22name%22%3A%20%22MyBLASTHit%22%7D%5D</code>Developers integrating JBrowse into larger project may find this feature useful for displaying results from other non-JavaScript-based applications (such as legacy web BLAST tools) in JBrowse.Features added to JBrowse in this way are available in a special data store named <code>url</code>, which can be specified in a track configuration by adding <code>"store":"url"</code>.</li> <li>Added support for an <code>addTracks</code> variable in the query string of the URL used to start JBrowse. This variable accepts track configurations in JSON format in the form:<code>[{"label":"mytrack","store":"url","type":"JBrowse/View/Track/HTMLFeatures"},...]</code>which, when URI-escaped and put in the query string, looks like:<code>addTracks=%5B%7B%22label%22%3A%22mytrack%22%2C%22store%22%3A%22url%22%2C%22type%22%3A%22JBrowse%2FView%2FTrack%2FHTMLFeatures%22%7D%5D</code></li> <li>Added "Save track data" option to Alignments2 tracks. This option should have been there all along, but somehow slipped through the cracks. Thanks to Valerie Wong for pointing this out at the 2013 GMOD Summer School!</li> <li>Statistics about a track's features are now shown in its "About this track" dialog, if available.</li> <li>Added support for a --reftypes argument to <code>prepare-refseqs.pl</code>, allowing you to search a database for reference sequences based on the type of the reference sequences, e.g. 'chromosome'. Thanks to Gaelen Burke at the 2013 GMOD Summer School for pointing out the need for this, and for assistance in testing the new feature.</li> <li>Added a <code>--gbk</code> option to <code>flatfile-to-json.pl</code> that accepts a GenBank-format text file as input for loading annotation data. Thanks to Justin Reese for the initial implementation of this.</li> <li>When formatting features with <code>flatfile-to-json.pl</code>, multi-valued feature attributes are now only flattened (renamed foo, foo2, foo3, etc) for "name", "id", "start", "end", "score", "strand", "description", and "note" attributes. Formerly, all attributes were flattened. This improves the default display of features that have many values for some attributes, such as Dbxrefs or GO terms.</li> <li>Further improved scrolling smoothness of HTML-based feature tracks.</li> <li><code>flatfile-to-json.pl</code> now supports a <code>--trackType</code> option that can be used to set the JavaScript track class that will be used for the formatted data (e.g. "JBrowse/View/Track/CanvasFeatures" to use the new, improved HTML5 canvas-based feature tracks).</li> <li><code>biodb-to-json.pl</code> configuration files now support a <code>trackType</code> configuration key in each track configuration that can be used to set the JavaScript track class that will be used for the formatted data (e.g. "JBrowse/View/Track/CanvasFeatures" to use the new, improved HTML5 canvas-based feature tracks).</li> <li><code>prepare-refseqs.pl</code> can now format reference sequences from a common .sizes (aka .len) file that is just a two-column tab-separated list of reference sequence names and their lengths, run like: bin/prepare-refseqs.pl --sizes myrefs.sizes</li> <li><code>prepare-refseqs.pl</code> can now format reference sequences from a gzipped GFF3 if the file's name ends with the suffix ".gz".</li> <li>Added a '--noSubfeatures' option for flatfile-to-json.pl to skip importing subfeatures (since <code>--getSubfeatures</code> is on by default for some time).</li> <li>The <code>style.label</code> configuration variable in HTMLFeatures (and CanvasFeatures) tracks can now accept a comma-separated string of field names in addition to a function callback. Defaults to 'name,id';</li> <li>The "Save track data" (data exporting) menu now has "Highlighted region" as one of the choices of which range to export, if there is something highlighted.</li> <li>The "JBrowse" link on the left side of the menu bar, and the browser title, now display the "About this browser" title instead of JBrowse, if <code>aboutThisBrowser</code> is set in the configuration. Thanks to Joanna Kelley at the 2013 GMOD Summer School for suggesting this.</li> <li>Tweaked styling of inactive track handles in the default Simple track selector to make them look less like pressable buttons. Thanks to Pedro Pagan at the 2013 GMOD Summer School for pointing out the need for this, and helping to brainstorm how the new styles should look.</li> <li>Horizontal mouse-wheel (or trackpad) events can now scroll the genome view horizontally. Thanks to Mara Kim for help testing this at the 2013 GMOD Summer School.</li> <li>The "content" of configurable information popups (such as can be shown when clicking on features) can now accept a dojo/Deferred or other promise object that will provide the content to be shown asynchronously.</li> <li>Added a <code>JBrowse/Store/SeqFeature/FromConfig</code> feature store adapter that can display feature data that is specified directly in configuration. This is mostly used to implement the support for <code>addFeatures</code> in the JBrowse URL, but some administrators and developers may find it conventient as well to define feature data directly in the JBrowse configuration.</li> <li>Added a <code>track.maxFeatureSizeForUnderlyingRefSeq</code> configuration variable, defaulting to 250 Kbp, that sets the maximum length of a feature for which the default feature detail popup will attempt to display the underlying reference sequence. Thanks to Colin Davenport for pointing out the need for this (issue #291).</li> <li>Added the ability to specify the file name when exporting track data to a file. Thanks to Daniel Kasenberg for implementing this.</li> <li>Added a <code>track.noExportFiles</code> configuration variable that, if set to true, disables exporting files from the "Save" menu of tracks.</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>Fixed a bug that prevented clicking on features in Alignments2 (and other canvas feature tracks) in Internet Explorer.</li> <li>Fixed a bad design decision with respect to track metadata stores. Before, a given metadata key ("Category", "Conditions", etc) was allowed to only be present in one source of track metadata (CSV file, configuration file, etc). The original thinking behind this was that it would be better for people to be forced to keep each kind of metadata in only one place. This was silly thinking. Thanks to the 2013 GMOD Summer School participants for helping me to see the error of my ways.</li> <li>Fixed a bug in which turning off the HTMLFeatures track's "Show Labels" did not remove labels for features with descriptions.</li> <li>Fixed a bug with <code>prepare-refseqs.pl</code> in which, when multiple definitions of a reference sequence are found (as in a GFF3 file with both ##sequence-region directives and a FASTA section), the seqChunkSize value is not recorded in refSeqs.json and the sequence bases cannot be displayed in the "Reference sequence" track.</li> <li>Fixed a synchronization bug in NCList-based feature data stores that causes some features to be missing when displaying with a CanvasFeatures track. This bug may also have affected 'Save track data' (data export) in some situations.</li> <li>Fixed a bug with GFF3 export in which the phase(!) column was missing. Thanks to Michael Campbell at the 2013 GMOD Summer School for helping track this down!</li> <li>Fixed another bug with GFF3 export in which an extra comma would sometimes be added at the beginning of GFF3 lines for some child features.</li> <li>Fixed a bug in which the global highlighted region was not correctly drawn when switching reference sequences.</li> <li>Fixed a minor bug in which the REST store backend did not coerce start, end, strand, and score to be numeric if the input JSON had them as strings.</li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/07/05/jbrowse-1-9-8-index.html">JBrowse 1.9.8 maintenance release</a></h1><p class="post-meta">July 5, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.9.8 has been released, with fixes for some minor issues, a performance improvement when many HTML-based tracks are open, and a new <code>yScalePosition</code> configuration option for all tracks can can be set to "left", "right", or "center" to change where the y-axis scale is displayed.</p> <p>Files for download:</p> <ul> <li><p><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=59" title="download JBrowse-1.9.8.zip">JBrowse-1.9.8.zip</a> - 5.1M file SHA1 ad7814dae6acfdc1393942dfcce5097c2db93cec</p></li> <li><p><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=60" title="download JBrowse-1.9.8-dev.zip">JBrowse-1.9.8-dev.zip</a> - 26M file SHA1 6e022fc7e8222e0a479044936334b4228f7cf25f Changes in this release:</p></li> <li><p>Removed "XX has no data for this chromosome" popup warning message. It was just annoying and not very useful.</p></li> <li><p>Added an optional "yScalePosition" element to track configs that allows configs with Y axes to have those axes positioned on the left or right side of the view, as well as in the center. Thanks to Alexis Grimaldi for making this change.</p></li> <li><p>Fixed a bug in which NCList-based tracks display with an error for reference sequences on which they have no data. Thanks to Michael Axtell for pointing this out.</p></li> <li><p>Improved GFF3 handling in the File->Open tool, fixed a bug in the GFF3 parser in which an empty (.) source column caused the GFF3 parser to crash.</p></li> <li><p>Improved scrolling speed when many HTML feature tracks are active.</p></li> <li><p>Fixed a bug in which the browser can fail to start for a reference sequence that has never been seen before.</p></li> <li><p>Fixed a confusing behavior in JBrowse/Store/SeqFeature/REST in which the URLs it constructs to fetch from did not always have a '/' where one would expect. Thanks to Alex Kalderimis for pointing this out.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/07/02/about-jbrowse-version-numbers-index.html">About JBrowse version numbers</a></h1><p class="post-meta">July 2, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>Just so everybody's on the same page, I thought I should point out that from 1.2.0 onward, JBrowse version numbers follow a predictable scheme that encodes a bit of information about what is contained in a release.</p> <p>JBrowse version numbers look like "A.B.C", where A, B, and C are positive integer numbers, which might have multiple digits. Each new JBrowse release increments one of these numbers.</p> <p>Incrementing C means that only bug fixes and small refinements have been added.</p> <p>Incrementing B means that major new features have been added, and C is reset to 0.</p> <p>Incrementin