JBrowse 1

JBrowse 1.13.1 maintenance release

March 28, 2018

JBrowse 1.13.1 has been released!

Files for download

Minor improvements

  • Gene, ProcessedTranscript, and Segments glyphs can now render third-level subfeatures (such as stop_codon_read_through features) as simple boxes that draw on top of the main segment glyph. Thanks to @mpoelchau for pointing out the need for this! (issue #584, @rbuels)

  • CanvasFeatures tracks, when guessing which glyph to show for a feature in a track that does not specify glyphs in its configuration, will now use a Segments glyph instead of a Box glyph if the feature in question has subfeatures, and is not otherwise recognized as a gene or processed transcript. @rbuels

  • Added a check in the setup.sh script for NodeJS >= 6 and NPM >= 3. (issue #1026, @rbuels)

  • Plugins that don't need CSS can now set jbrowsePlugin.css to false in their package.json files to prevent JBrowse trying to load their css/main.css file, if they don't use any CSS. (@rbuels)

  • Add ability for the CanvasFeatures feature labels to stay visible on the screen. (issue #390, issue #971, @cmdcolin, @rbuels)

  • Improve VCF tracks support for GVCF generated by GATK, and fix a number of related VCF details display bugs. (issue #991, @cmdcolin)

  • generate-names.pl now supports indexing GFF3 files, enabling better use of GFF3Tabix tracks. Thanks to @billzt for the initial implementation! (issue #780, issue #900, @rbuels)

  • CanvasFeatures ProcessedTranscript and Gene glyphs now support a "style→utrHeightPercent" configuration variable that sets the percentage of the overall feature's height that UTRs have. This was previously hardcoded to 65, now it is customizable, defaulting to its old value of 65. @rbuels

Bug fixes

  • Updated NeatCanvasFeatures and NeatHTMLFeatures plugins to support a gradient configuration variable, fix rendering of outrons, restore their default gradient-drawing behavior, disable gradients by default on Alignments and Alignments2 track types, and clean up their documentation. (issue #931, issue #982, issue #985, issue #931, issue #992, issue #1011, @enuggetry)

  • Fixed a bug with plugin loading that was preventing some plugins from working correctly. (issue #1025, @rbuels)

  • flatfile-to-json.pl will now refuse to format a track if the trackLabel contains a '/' character. Thanks to @dytk2134 for pointing this out, and @cmdcolin for the fix! (issue #1023, @cmdcolin)

  • Fixed a bug in which the viewing location would not be preserved across page reloads if generate-names.pl had not been run, or a names store had not otherwise been defined. Thanks to @cmdcolin for the bug report. (issue #1016, @rbuels)

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