JBrowse 1.10.8 maintenance release

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.

Bug fixes

  • 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.

About Robert Buels

JBrowse Lead Developer
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