@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 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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/2014/01/07/jbrowse-1-11-1-index.html">JBrowse 1.11.1 maintenance release</a></h1><p class="post-meta">January 7, 2014</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.11.1 has been released, with a number of bug fixes and some nice improvements to Alignments2 tracks. Most of the Alignments2 improvements were thought up by Keiran Raine at Sanger, thanks Keiran! Thanks also to Cris Lawrence and Richard Hayes, who were helpful in finding some other bugs and opportunities for improvements.</p> <p>Files for download:</p> <ul> <li><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=89" title="download JBrowse-1.11.1.zip">JBrowse-1.11.1.zip</a> - 4.7M file SHA1 9ae684b90fa033b76072f9fdad91bdb6a1d8180a</li> <li><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=90" title="download JBrowse-1.11.1-dev.zip">JBrowse-1.11.1-dev.zip</a> - 26M file SHA1 23b6d80b92ac9259994287a7c307860b184a21f5</li> </ul> <h2><a class="anchor" aria-hidden="true" id="minor-improvements"></a><a href="#minor-improvements" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Minor improvements</h2> <ul> <li><p>Alignments2 tracks now include right-click menu items to view the location of an alignment's mate pair or next segment in a popup or a new tab. Thanks to Keiran Raine for suggesting this (<a href="https://github.com/gmod/jbrowse/issues/406">issue #406</a>).</p></li> <li><p>Alignments2 tracks now draw gaps and deletions in reads regardless of zoom level, as long as the alignment is at least 3 pixels wide in the display. Thanks to Keiran Raine for pointing out the need for this (<a href="https://github.com/gmod/jbrowse/issues/403">issue #403</a>).</p></li> <li><p>Added support for a <code>histograms.max</code> variable for CanvasFeatures-based tracks that can be used to manually set the max value of a histogram display. Thanks to Keiran Raine for pointing out the need for this.</p></li> <li><p>Added support for drawing clip markers (with their color set by <code>histograms.clip_marker_color</code>) in CanvasFeatures-based tracks. Thanks to Keiran Raine for pointing out the need for this (<a href="https://github.com/gmod/jbrowse/issues/402">issue #402</a>).</p></li> <li><p>Canvas-based feature tracks now try to draw histograms, if available, when the data backend throws a data-overflow error (like when the BAM backend exceeds the chunkSizeLimit). Thanks to Keiran Raine for motivating this (<a href="https://github.com/gmod/jbrowse/issues/405">issue #405</a>).</p></li> <li><p>Make it easier to set JS loading baseUrl by moving it into the initial dojo configuration. Thanks to Jillian Rowe for pointing out the need for this.</p></li> <li><p>Enhanced new text-based config syntax to support arrays of values in a list like:</p> <p>[trackMetadata] sources =</p> <ul> <li>data/mymeta.csv</li> <li>data/more_meta.csv</li> </ul></li> </ul> <h2><a class="anchor" aria-hidden="true" id="bug-fixes"></a><a href="#bug-fixes" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Bug fixes</h2> <ul> <li><p>When a number is typed into the location box, JBrowse first checks if it is the name of a feature in the names index, and only interprets it as a coordinate if it is not found in the names index. Thanks to Richard Hayes for pointing this out (<a href="https://github.com/gmod/jbrowse/issues/407">issue #407</a>).</p></li> <li><p>Fixed bug that caused client-side GFF3 tracks to appear as "Loading" forever if the GFF3 is malformed (like malformed GFF3 files that are opened with the File->Open tool).</p></li> <li><p>Fixed bug in which no default value for <code>maxFeatureSizeForUnderlyingRefSeq</code> was being set, which made default feature detail popups try to fetch and display a feature's underlying reference sequence even if it is way too large, unless the variable was set explicitly in the configuration.</p></li> <li><p>JBrowse now shows a more understandable error message when trying to open an uncompressed BAM file. Thanks to Keiran Raine for pointing this out (<a href="https://github.com/gmod/jbrowse/issues/404">issue #404</a>).</p></li> <li><p>Fixed jbrowse.conf faceted track selector configuration examples not working as written. Thanks to Cris Lawrence for pointing this out.</p></li> <li><p>Fixed a bug in which right-clicking on feature labels in an HTMLFeatures-based track did not bring up the right-click menu for a feature. Thanks to Cris Lawrence for pointing this out (<a href="https://github.com/gmod/jbrowse/issues/408">issue #408</a>).</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/12/19/jbrowse-1-11-0-index.html">JBrowse 1.11.0: hierarchical track selector, easier configuration, summary mode</a></h1><p class="post-meta">December 19, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.11.0 is out today, with some major new features, and, as always, quite a lot of smaller bugfixes and improvements.</p> <p>But first, the download links:</p> <ul> <li><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=87" title="download JBrowse-1.11.0.zip">JBrowse-1.11.0.zip</a> - 4.7M - <a href="https://jbrowse.org/docs/tutorial_classic.html" title="JBrowse Quick-Start">installation quick-start tutorial</a></li> </ul> <div>file SHA1 49fb7be687c5dff7857d080bf8503cddedea4e51</div> * [JBrowse-1.11.0-dev.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=88 "download JBrowse-1.11.0-dev.zip") - 26M <div>file SHA1 daa4de81cb11f3d1f0406887a1fbc06efdd44fff</div> Firstly, JBrowse has added** a third track selector type** alongside the existing Simple (small) and Faceted (large) track selectors **called Hierarchical**. It looks like the old Simple track selector (which was the default), except it pays attention to the "category" key in a track's metadata, and if it is present, it organizes the tracks into nested, collapsible panes based on that. Also, instead of the drag-and-drop paradigm used by the Simple track selector, the Hierarchical track selector turns tracks on and off by just checking and unchecking the box next to each track. I think the checkboxes are probably easier for new users to understand, as well, the Hierarchical track selector is now enabled by default. Those that prefer the old Simple selector can always turn it on by setting trackSelector.type to "Simple" in the jbrowse_conf.json file or the new jbrowse.conf file, which brings me to my next item. <p>Secondly, JBrowse now has a <strong>additional text configuration format</strong> that is designed to be easier to hand edit, and can coexist and interoperate with existing JSON configuration files. Users of GBrowse will find the syntax very familiar, since its design borrows heavily from GBrowse's configuration syntax. Here's a side-by-side comparison of what you would write in the old JSON and new text configuration formats to make JBrowse use the old Simple track selector.</p> <table> <tbody> <tr> <th>jbrowse_conf.json</th> <th>jbrowse.conf</th> </tr> <tr> <td> <pre>"trackSelector": { "type": "Simple" }</pre> </td> <td> <pre>[trackSelector] type = Simple</pre> </td> </tr> </tbody> </table> It's easier to configure tracks in the new format, as well. Here's a typical BAM Alignments2 track configuration in both formats, for comparison. <table> <tbody> <tr> <th>trackList.json</th> </tr> <tr> <td> <pre>"tracks": [ { "storeClass" : "JBrowse/Store/SeqFeature/BAM", "urlTemplate" : "../../raw/volvox/volvox-sorted.bam", "label" : "volvox-sorted-bam", "type" : "JBrowse/View/Track/Alignments2", "key" : "My BAM track" } ]</pre> </td> </tr> <tr> <th>tracks.conf</th> </tr> <tr> <td> <pre>[tracks.volvox-sorted-bam] storeClass = JBrowse/Store/SeqFeature/BAM urlTemplate = ../../raw/volvox/volvox-sorted.bam type = JBrowse/View/Track/Alignments2 key = My BAM track</pre> </td> </tr> </tbody> </table> And for the final headline feature of this release, JBrowse CanvasFeatures, CanvasVariants, and Alignments2 tracks can now be configured to show** feature density histograms or coverage plots** when zoomed too far out to display individual features. They can take this quantitative data from** any type of JBrowse data store** (including REST stores), but most users would want to use a BigWig store. One caveat: this isn't a full-featured quantitative display like a Wiggle/XYPlot track, so quantitative values need to all be greater than 0, and all you can really change about how it looks is its color. Here's an example in the new text configuration syntax of an Alignments2 track that will display either alignments from a BAM file or a coverage plot from a BigWig file, depending on zoom level. <pre>[tracks.my-bam-with-coverage] <p>storeClass = JBrowse/Store/SeqFeature/BAM urlTemplate = my_alignments.bam</p> <p>type = JBrowse/View/Track/Alignments2 key = My BAM track</p> <p>histograms.storeClass = JBrowse/Store/SeqFeature/BigWig histograms.urlTemplate = my_alignments.bam.coverage.bw histograms.description = coverage plot histograms.color = #dcdcdc</pre> Of course, there are many smaller improvements and bug fixes. Read on for the complete release notes.</p> <h1><a class="anchor" aria-hidden="true" id="release-1110"></a><a href="#release-1110" 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>Release 1.11.0</h1> <h2><a class="anchor" aria-hidden="true" id="major-improvements"></a><a href="#major-improvements" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Major improvements</h2> <ul> <li>Introduced density/coverage histogram support for CanvasFeatures, CanvasVariants, and Alignments2 tracks. These track types now support an optional <code>histograms</code> configuration subsection that can contain a definition for a second datastore that holds quantitative data (usually either coverage depth or feature density) to be displayed when zoomed further out than <code>featureScale</code> (or if <code>featureScale</code> is not set, the scale determined by the store's feature density divided by <code>maxFeatureScreenDensity</code>). Thanks to Richard Hayes for pushing hard for this feature.</li> <li>Added a new "Hierarchical" track selector that shows tracks in a hierarchy of collapsible categories, which is now the default track selector. To assign categories and subcategories to your tracks, set <code>category</code> or <code>metadata.category</code> attributes on each configured tracks in your <code>trackList.json</code>. Thanks to the many users who have requested this at one time or another.</li> <li>JBrowse now supports a new plaintext configuration format that users of GBrowse will find very familiar, since it is designed to be very similar to it. This syntax is also much easier to hand-write than JSON. The JSON configuration syntax is not going away, and will continue to be supported.</li> </ul> <p>Thanks to Erik Derohanian for the original implementation of this configuration adaptor, and Richard Hayes and Keiran Raine for motivating the work to polish and more fully integrate it.</p> <ul> <li>Variables in configuration files can now be based on the contents of other variables. For example, setting</li> </ul> <p>"myCustomVariable": "/some/custom/path", "include": "{myCustomVariable}/conf.json"</p> <p>will try to include a configuration file located at "/some/custom/path/conf.json". Interpolation is done as the final step in configuration loading, so variables can come from anywhere in the configuration.</p> <ul> <li>When JBrowse is started, if there are no reference sequences found in the default <code>dataRoot</code>, but the dataset selector is configured, JBrowse shows a simple list of links to available datasets instead of the "Congratulations, JBrowse is on the web" page. Thanks to Saulo Aflitos for the idea and its initial implementation.</li> <li>For users wishing to convert existing JSON configuration files to the new format, there is a new script, <code>bin/json2conf.pl</code>, that does a fair job. Run <code>bin/json2conf.pl -?</code> for details on how to use it.</li> <li>Added a new REST backend for name lookup and autocompletion. See <a href="http://gmod.org/wiki/JBrowse_Configuration_Guide#JBrowse_REST_Names_API">http://gmod.org/wiki/JBrowse_Configuration_Guide#JBrowse_REST_Names_API</a> for details. Thanks to Erik Derohanian for implementing this, and Ben Booth for suggesting an API design (<a href="https://github.com/gmod/jbrowse/issues/267">issue #267</a>).</li> <li>Major performance and scalability improvements for <code>generate-names.pl</code>. Now uses a different algorithm that is faster and more scalable than before, and no longer relies on BerkeleyDB for temporary storage. This should also alleviate the need to run generate-names.pl with <code>--safeMode</code> in Perl 5.10 and earlier. In fact, the <code>--safeMode argument</code> to generate-names.pl no longer has any effect. Thanks to Cris Lawrence for pointing out the continuing need for more scalability.</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>Detail popups for CanvasVariants and HTMLVariants tracks now display the reference sequence itself instead of just "ref" in genotype displays. Thanks to Cris Lawrence for requesting this.</li> <li>Added a "save as FASTA" button to default feature detail popups that downloads a FASTA file with the displayed piece of reference sequence (<a href="https://github.com/gmod/jbrowse/issues/299">issue #299</a>).</li> <li><code>chunkSizeLimit</code> for VCF files now defaults to 1 MiB. It used to be 15 MiB, which was really far too big for browsers to handle.</li> <li>Added support for a <code>--nameAttributes</code> argument to <code>flatfile-to-json.pl</code> that takes a comma-separated list of feature attributes to index for name searching and completions, or 'none' to not make names searchable.</li> <li>Added support for a <code>nameAttributes</code> variable in <code>biodb-to-json.pl</code> track configurations that can be set to an array of feature attribute names to to index for name searching and completions, or 'none' to not make names searchable.</li> <li>Add a <code>--category</code> argument to bin/wig-to-json.pl that can be used to set the <code>metadata.category</code> of a track.</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 in NCList data backed in which feature histograms were often calculated very incorrectly.</li> <li>Fixed a bug in the VCF data backend that caused not all VCF features to be shown in some files at some zoom levels.</li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/12/10/jbrowse-1-10-12-index.html">JBrowse 1.10.12 maintenance release (please upgrade!)</a></h1><p class="post-meta">December 10, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.10.12 has been released, and <strong>we are asking all users of JBrowse <del>1.10.7</del> 1.10.10 and higher to please upgrade to this release as soon as possible</strong>.</p> <p>The story behind this is a bit embarassing: I discovered today that JBrowse releases <del>1.10.7 through</del> 1.10.10 and 1.10.11 shipped with usage analytics reporting disabled. This is a little piece of code that tracks how many installations and users of JBrowse there are, and the data it provides is absolutely crucial for the JBrowse project, because we use it to try to convince funding agencies that JBrowse is a project worth funding.</p> <p>So, yes ... this release has analytics reporting re-enabled. There are also a few other minor improvements and bug fixes. Please upgrade to this ASAP if you are using JBrowse <del>1.10.7, 1.10.8, 1.10.9,</del> 1.10.10 or 1.10.11, because we really need that analytics data.</p> <p>**Edit (Dec 11): **realized just now that only 1.10.10 and 1.10.11 were affected. Forgot to account for branching and merging last night.</p> <p>Files for download:</p> <ul> <li><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=85" title="download JBrowse-1.10.12.zip">JBrowse-1.10.12.zip</a> - 4.6M file SHA1 6a73716eea1df063beec0bb0a03402e92e027317</li> <li><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=86" title="download JBrowse-1.10.12-dev.zip">JBrowse-1.10.12-dev.zip</a> - 26M file SHA1 1cd196de451ac246ab26c8b36bd4babaa9ffc842</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><code>bam-to-json.pl</code> and <code>flatfile-to-json.pl</code> now support a <code>--metadata</code> argument that can add a <code>metadata</code> stanza to track configurations they generate.</li> <li>Multi-valued attributes in default feature detail popups are displayed as a string of boxes, each containing a value, to avoid misinterpretation. Thanks to Cris Lawrence for pointing out the need for this.</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>Re-enabled usage analytics reporting, which had been disabled by a stray piece of debugging code since the 1.10.7 release.</li> <li>Fixed a bug in which the tooltip in canvas-based feature tracks would sometimes display incorrect label or description text.</li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/12/03/jbrowse-1-10-11-index.html">JBrowse 1.10.11 maintenance release</a></h1><p class="post-meta">December 3, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.10.11 has been released, with many bug fixes and better support for spliced alignments in SNPCoverage tracks.</p> <div style="padding: 2em 1em; margin: 1em; border: 1px solid #eee; background: #fcfcfc">(Download disabled. Please download the[ 1.10.12 release](http://jbrowse.org/jbrowse-1-10-12/ "JBrowse 1.10.12 maintenance release") or later instead.) </div> <h2><a class="anchor" aria-hidden="true" id="minor-improvements"></a><a href="#minor-improvements" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Minor improvements</h2> <ul> <li><p>Made the sequence track's "zoom in to see sequence" placeholder take up less vertical space. Thanks to Scott Cain for pointing out that making it be the same height as it will eventually be when zoomed in to base level is silly.</p></li> <li><p>By default highlighting features after searching for them by name is now turned off. Set the <code>highlightSearchedRegions</code> top-level conf variable to <code>true</code> to turn this back on. Turns out, most people seem not to like this behavior. Thanks to Gregg Helt and Cris Lawrence for pointing this out.</p></li> <li><p><code>SNPCoverage</code> tracks now correctly display "skipped" regions in alignments, such as those produced by TopHat. Thanks to Josh Orvis, Gustavo Cerquiera, and others for reminders that this was still an issue.</p></li> <li><p><code>SNPCoverage</code> tracks now provide per-strand counts of "reference" reads at each position, like they already were providing for reads with mismatches.</p></li> <li><p><code>SNPCoverage</code> tracks now accept a <code>mismatchScale</code> configuration variable that sets the viewing scale (i.e. zoom level, pixels per bp) above which base-level mismatches will be drawn. Defaults to 1/10. Making this value larger can speed up SNPCoverage tracks for high-coverage data at the cost of needing to zoom in further to see mismatches.</p></li> <li><p>setup.sh now uses <code>curl</code> for downloading things instead of <code>wget</code>, since <code>curl</code> is more widely available. Thanks to Keiran Raine for suggesting and implementing this (<a href="https://github.com/gmod/jbrowse/issues/393">issue #393</a>).</p></li> </ul> <h2><a class="anchor" aria-hidden="true" id="bug-fixes"></a><a href="#bug-fixes" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Bug fixes</h2> <ul> <li><p>Fixed a bug in which <code>generate-names.pl</code> would sometimes report the incorrect number of hashing bits in verbose output, and would sometimes use the number of hashing bits for an existing index even if that index was being regenerated. Thanks to Richard Hayes for pointing out the incorrect log output.</p></li> <li><p>Fix <code>generate-names.pl</code> crashing on some older versions of Perl with an error like <code>Bareword "POSIX::O_RDONLY" not allowed while "strict subs" in use</code>. Thanks to Chris Childers for pointing this out.</p></li> <li><p>Fix <code>setup.sh</code> failing on some older versions of Perl. It now runs <code>generate-names.pl</code> with the <code>--safeMode</code> flag.</p></li> <li><p>Fixed a bug where the value display in SNPCoverage tracks would sometimes report "NaN%" for the reference when no reads cover a region.</p></li> <li><p>Fixed a bug in which activating rubberband zooming using the SHIFT key while in highlighting mode would cause all the tracks to be dragged when attempting to highlight a region afterward. Thanks to Erik Derohanian for pointing out and fixing this (<a href="https://github.com/gmod/jbrowse/issues/387">issue #387</a>).</p></li> <li><p>Fixed the location of the dojo/nls directory in release zipfiles. Was erroneously in src/nls, supposed to be src/dojo/nls. Thanks to Matt Bomhoff for pointing this out.</p></li> <li><p>The in-memory GFF3 parser now copes with a missing newline at the end of a GFF3 file. Previously, the last line was ignored if it did not end with a newline character. Thanks to Colin Davenport for pointing this out (<a href="https://github.com/gmod/jbrowse/issues/394">issue #394</a>).</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/11/21/jbrowse-1-10-10-index.html">JBrowse 1.10.10 maintenance release</a></h1><p class="post-meta">November 21, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.10.10 has been released, with new compression support in <code>generate-names.pl</code>, configurable inter-track spacing, and quite a few bug fixes.</p> <div style="padding: 2em 1em; margin: 1em; border: 1px solid #eee; background: #fcfcfc">(Download disabled. Please download the[ 1.10.12 release](http://jbrowse.org/jbrowse-1-10-12/ "JBrowse 1.10.12 maintenance release") or later instead.) </div> <h2><a class="anchor" aria-hidden="true" id="minor-improvements"></a><a href="#minor-improvements" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Minor improvements</h2> <ul> <li><p>Spacing between tracks is now configurable by setting <code>view.trackPadding</code> in the configuration. Thanks to Chenchen Zhu for suggesting this (<a href="https://github.com/gmod/jbrowse/issues/377">issue #377</a>).</p></li> <li><p>If reference sequences are defined, but no tracks are yet added, JBrowse will start normally instead of going to the "Congratulations, JBrowse is on the web" page.</p></li> <li><p><code>generate-names.pl</code> now supports a <code>--compress</code> option that compresses the name index files to save server disk space. Thanks to Richard Hayes for pointing out the need for this (<a href="https://github.com/gmod/jbrowse/issues/378">issue #378</a>).</p></li> </ul> <h2><a class="anchor" aria-hidden="true" id="bug-fixes"></a><a href="#bug-fixes" aria-hidden="true" class="hash-link"><svg class="hash-link-icon" aria-hidden="true" height="16" version="1.1" viewBox="0 0 16 16" width="16"><path fill-rule="evenodd" d="M4 9h1v1H4c-1.5 0-3-1.69-3-3.5S2.55 3 4 3h4c1.45 0 3 1.69 3 3.5 0 1.41-.91 2.72-2 3.25V8.59c.58-.45 1-1.27 1-2.09C10 5.22 8.98 4 8 4H4c-.98 0-2 1.22-2 2.5S3 9 4 9zm9-3h-1v1h1c1 0 2 1.22 2 2.5S13.98 12 13 12H9c-.98 0-2-1.22-2-2.5 0-.83.42-1.64 1-2.09V6.25c-1.09.53-2 1.84-2 3.25C6 11.31 7.55 13 9 13h4c1.45 0 3-1.69 3-3.5S14.5 6 13 6z"></path></svg></a>Bug fixes</h2> <ul> <li><p><code>generate-names.pl</code> now uses IO::Uncompress::Gunzip instead of PerlIO::gzip to read compressed VCF files. This fixes a bug in which only the first few hundred names in a VCF were indexed. Thanks to Cris Lawrence for pointing this out (<a href="https://github.com/gmod/jbrowse/issues/380">issue #380</a>).</p></li> <li><p>Fixed a bug in which <code>generate-names.pl</code> would crash if run with <code>--incremental</code> and no existing names index. Thanks to Richard Hayes for pointing this out (<a href="https://github.com/gmod/jbrowse/issues/379">issue #379</a>).</p></li> <li><p>Fixed a bug in which <code>generate-names.pl</code> would sometimes choose the wrong number of hash bits when performing incremental updates, leading to the old data being lost. Thanks to Richard Hayes for lots of help troubleshooting this.</p></li> <li><p>Fixed bug where other tracks are visible underneath pinned tracks when the display is scrolled down. Thanks to Ed Lee for pointing this out.</p></li> <li><p>Fixed a bug in which tooltip does not hide after the mouse leaves a Wiggle track in Safari 5 and 6. Thanks to Charles Girardot for pointing this out.</p></li> <li><p>Fixed a bug in which the <code>main.css</code> file for plugins was not being correctly loaded in some installations. Thanks to Matt Bomhoff for pointing this out.</p></li> </ul> </span></div></article></div><div class="post"><header class="postHeader"><h1 class="postHeaderTitle"><a href="/blog/2013/11/08/jbrowse-1-10-9-index.html">JBrowse 1.10.9 maintenance release</a></h1><p class="post-meta">November 8, 2013</p><div class="authorBlock"></div></header><article class="post-content"><div><span><p>JBrowse 1.10.9 has been released, with new incremental-updating support in <code>generate-names.pl</code>, along with some other bug fixes and small improvements.</p> <p>Files for download:</p> <ul> <li><a href="/wordpress/wp-content/plugins/download-monitor/download.php?id=79" title="download JBrowse-1.10.9.zip">JBrowse-1.10.9.zip</a> - 4.6M file SHA1 e05f599c8692489e7c184cfd6c340afc79519a38</li> <li><a href="http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=80" title="download JBrowse-1.10.9-dev.zip">JBrowse-1.10.9-dev.zip</a> - 26M file SHA1 e74d9b8ab21aa31e9ce09ff996ec45916b934821</li> </ul> <h2><a cl