JBrowse 1.13.1

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, pull #971, @cmdcolin, @rbuels)

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