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@gmod/jbrowse

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JBrowse - client-side genome browser

jbrowse.org

GMOD/jbrowse

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--- layout: post title: JBrowse 1.6.5 bugfix release date: 2012-10-26 tags: ["Software releases"] --- I'm pleased to announce the release of JBrowse 1.6.5, containing some small new features, plus fixes for some issues in the [1.6.4 release](http://jbrowse.org/jbrowse-1-6-4-bugfix-release/ "JBrowse 1.6.4 bugfix is also coming along very soon, with a (we hope!) very impressive set of new features. Stay tuned.release"). Files for download: * [JBrowse-1.6.5-min.zip](/wordpress/wp-content/plugins/download-monitor/download.php?id=23 "download JBrowse-1.6.5-min.zip") - 2.8M * [JBrowse-1.6.5-full.zip](http://jbrowse.org/wordpress/wp-content/plugins/download-monitor/download.php?id=24 "download JBrowse-1.6.5-full.zip") - 27.3M Changes in this release: * The location box now shows the **length of the currently visible** ** region** in parentheses. For example: `ctgB:1244..3566 (2.32 Kb)`. Thanks to Karsten Hokamp for the suggestion! * The **arrow keys** on the keyboard can now be used to pan and scroll around the genome view. * Wiggle track mouseover cursors now display the score with only 6 significant digits, avoiding confusion over approximations introduced by scores being converted to IEEE floating-point numbers (as for BigWig files) and back to text. * The faceted track selector now renders any HTML that may be present in the track metadata by default. To turn this off, it now accepts an `escapeHTMLInData` option that, if set to `true` or `1`, will not render the HTML, but will instead display the raw code (issue #145). * Upgraded to a more recent version of jszlib, which contains some important bugfixes (issue #157). * Fixed bug dealing with very large regions with the same value in canvas-based Wiggle tracks (also issue #157). * `prepare-refseqs.pl` now by default uses a **more scalable directory** ** structure for storing sequences**. This fixes problems some users were experiencing with large numbers of reference sequences (issue #139). * `ucsc-to-json.pl` now supports a `--primaryName` option allowing the users to **alter which UCSC data field is displayed by JBrowse as** ** the primary name** of the features in a track. Also, `ucsc-to-json.pl` now treats as indexable names all UCSC data columns called "name", "alias", or "id" followed by zero or more digits. Thanks to Steffi Geisen for this suggestion. * Fixed "Duplicate specification" warnings coming from `flatfile-to-json.pl` and `remove-track.pl`. * Fixed bugs in which both the first few and the last few bases of a reference sequence were not displaying correctly in a DNA track.