JBrowse-1.12.0: Open new genome from FASTA, in-line refseqs, NeatFeatures, Desktop

We are happy to announce JBrowse 1.12.0 release! This new release includes some exciting new features including the ability to load new genomes from FASTA and indexed FASTA formats; in-line refseqs, and server-free desktop applications for Windows and OSX (based on Electron).  New plugins beautifully enhances feature rendering with intron hats and gradients in both HTML and canvas tracks, provide URL links to call up tracks by category URL, among others.  Improvements include the ability to load custom histograms for tracks loaded from flatfile-to-json.pl; a new wiggle track option scoreType: ‘avgValue’, which helps preserve continuity when zooming in on certain tracks like GC-content; and the ability to specify the set of startCodons and stopCodons in the config.  In addition, several bugs have been addressed.

New features

  • Added ability to open a new genome in FASTA format from the browser. Also supports indexed FASTA. Thanks to Bradford Powell for the original indexed FASTA contribution (issue #495issue #647).
  • Support for inline reference sequence configurations.
  • Created stand-alone desktop version of JBrowse using the Electron platform for OSX, Windows (issue #647).

New plugins

  • NeatHTMLFeatures – Add the drawing of introns and gradient features to HTML tracks.
  • NeatCanvasFeatures – Add the drawing of introns and gradient features to Canvas tracks.
  • CategoryUrl – Implements a cat= URL option to display tracks for a given category (issue #618).
  • DebugEvents – a plugin to display global publish and milestone events on the debug console.
  • HideTrackLabels – Adds a toolbar button to toggle the display of track labels on and off (issue #614).

Minor improvements

  • Added new menu format to support loading your own genome. The open genome option can be hidden via hideGenomeOption in config, and the classic menu style can be restored via classicMenu in config.
  • Added ability to load custom histograms for tracks loaded from flatfile-to-json.pl (i.e. override a pre-existing histogram store). See (issue #612).
  • Added these options to add-bw-track.pl –clip_marker_color , –bg_color , –height (issue #510).
  • Added an option for Wiggle tracks, scoreType: ‘avgValue’, which helps preserve continuity when zooming in on certain tracks like GC-content. It complements the scoreType: ‘maxValue’ introduced in 1.11.6. Thanks to Han Lin for the pull request (issue #504).
  • Clarify track filter box description and feature search box “placeholder” text. (issue #611)
  • Implement option to have a separate location box from search box (issue #611issue #652).
  • Move CSS files into css folder.
  • Added ability to specify the set of startCodons and stopCodons in the config files. Thanks to Eric Rasche for the contribution (issue #657)!

Bug fixes

  • Add Travis-CI and jshint linting to build (issue #628).
  • Fixed a bug where the BAM popup boxes would display some incorrect info due to byte packing. Thanks to Thomas Downs for contributing the fix.
  • Fixed a bug where grid lines wouldn’t render at some particular zoom levels (issue #514).
  • Fixed a bug where the user’s –workdir parameter would be deleted which could have unintended side effects if the –workdir was pointing to important data, but this is uncommon (issue #563).
  • Allow falsey values to be used in browser.cookie.
  • Fix minor issue where sometimes the length field of refSeqs.json was missing.
  • Fix some issues that occurred when a reference sequence was named ‘0’ (issue #662issue #610).
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