JBrowse 1

JBrowse 1.11.2 maintenance release

February 10, 2014

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!
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