JBrowse 1.11.2 maintenance release

JBrowse 1.11.2 has been released, with some new controls to adjust the size of quantitative tracks (thanks to Evan Briones at University of Arizona!), added support for the new text-based tracks.conf files to generate-names.pl, and quite a few other small improvements.

Files for download:

Minor improvements

  • Added some user interface elements to set the height in pixels of a
    single quantitative track, or of all visible quantitative tracks.
    Thanks to Evan Briones for implementing this!
  • Added a JBrowse/View/FeatureGlyph/Diamond glyph that draws
    diamond-shaped features instead of boxes. Thanks to OICR Co-op
    student Kevin Mohamed for implementing this!
  • Reference sequence tracks now display a “no sequence” message
    instead of a bunch of blank blocks when the reference sequence
    basepairs aren’t available. Thanks to Kevin Mohamed for
    implementing this (issue #422).
  • Persistent session state is now stored on a per-dataset basis,
    which improves user experience when switching between multiple
    datasets in JBrowse. Thanks to Richard Hayes for pointing this
    issue out, and Kevin Mohamed for the fix (issue #410).
  • “Hide sites not passing …” settings in VCF track menus now show
    the filter’s long description when hovered over. Thanks to Keiran
    Raine for suggesting this (issue #420).
  • Tweaked display of track labels and added a slight border at the
    top edge of each track to make it more clear which track data
    belongs to. Thanks to Keiran Raine for suggesting this, and Kevin
    Mohamed for the initial implementation (issue #432).
  • Added a --config option to flatfile-to-json.pl that accepts
    additional configuration variables that will be merged into the top
    level of the track configuration. Thanks to Mikael Brandström
    Durling for the initial implementation of this.

Bug fixes

  • generate-names.pl now indexes VCF files from track definitions in
    tracks.conf files. Thanks to Paul Halle for pointing this out
    (issue #434).
  • Added a missing dependency for the server side formatting tools on
    List::MoreUtil 0.28 or higher. Thanks to Cris Lawrence and Keiran
    Raine for troubleshooting this!

About Robert Buels

JBrowse Lead Developer
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