JBrowse 1.10.8 maintenance release

October 25, 2013

JBrowse 1.10.8 has been released, with an important bugfix for generate-names.pl, better REST data store feature caching, and more.

Files for download:

Minor improvements

Added a new navigateTo action usable for customizing feature left-clicks and right-click menus. Thanks to Scott Cain for requesting this.
Added a new feature_range_cache option for the REST data backend. If set to true, the REST backend will more aggressively cache ranges of feature data. Thanks to Daniel Troesser for pointing out the need for this (issue #369).
maker2jbrowse now, by default, runs generate-names.pl to generate names indexes. Also added a --no_names_index option to turn this off. Thanks to Josie Reinhardt for making me notice this was missing.
Tweaked generate-names.pl default indexing parameters to emphasize indexing speed more. Now defaults to a smaller average file size for the on-disk JSON files it produces, which is much faster to generate and write (up to 8 or 10x faster). However, the on-disk index is about 2-2.5x larger overall.
Removed support for the --refids command-line argument to prepare-refseqs.pl, which has probably never really worked.
Improved prepare-refseqs.pl support for Bio::DB::Das::Chado database backends. Thanks to Gwendoline Andres for helping troubleshoot this.

Fixed generate-names.pl making incorrect name indexes when using 16 or more bits of hashing (when the number of index entries exceeds about 4 million). Thanks to Josie Reinhardt for helping troubleshoot this (issue #370).
The faceted track selector no longer refuses to display track unique labels even if they are explicitly included in the displayColumns setting.