JBrowse 1.9.5 maintenance release

JBrowse 1.9.5 has been released, with some small new features, and fixes for many small issues.

Files for download:

Changes in this release:

  • Added a trackSelector.initialSortColumn configuration variable
    to the faceted track selector that can be used to set the initial
    sort order for the grid in the faceted track selector. Thanks to
    Alexie Papanicolaou for suggesting this.

  • Made Wiggle density tracks indicate out-of-range values using
    separate clip markers at the top and bottom of the color field,
    rather than showing the out-of-range region as a third color (or
    black or white). Thanks to Gregg Helt for suggesting this.

  • Added support for a quickHelp configuration variable that lets
    administrators customize the contents of the Help->General dialog.
    Thanks to Gregg Helt for suggesting this.

  • Rewrote GFF3 direct-access backend to make it more
    standards-compliant and capable of parsing all attributes of a
    feature. Thanks to Jillian Rowe and Colin Davenport for pointing
    out the need for this.

  • Fixed arrowheads on HTMLFeatures not always being visible when the
    viewing region is being panned back and forth. Thanks to Gregg
    Helt for pointing this out.

  • Fixed a bug in which editing a track’s configuration JSON through
    the track menu when the faceted track selector was enabled
    sometimes caused another track to be deactivated. Thanks to Steffi
    Geisen for pointing this out.

  • Fixed a subtle bug in which not completing a track-dragging gesture
    from the Simple track selector into the genome view caused the
    track handle to not disappear from the track selector when the
    track is turned on later. Thanks to Gregg Helt for pointing this
    out.

  • Fixed a bug in which prepare-refseqs.pl can crash when used with
    Bio::DB::Das::BioSQL. Thanks to Brian Osborne for contributing the
    fix.

  • Fixed failures of setup.sh legacy BAM support installation caused
    by samtools taking down their old SourceForge subversion
    repository.

  • Fixed a bug in which highlighted regions were not always drawn
    correctly at initial load time. Thanks to Steffi Geisen for
    pointing this out.

  • Added support for a plugins->[]->location configuration
    attribute, making it possible for plugins to be loaded from outside
    the JBrowse plugins directory.

  • Fixed a bug in which Wiggle track value displays behaved a bit
    oddly with some kinds of mouse movements. Thanks to Gwendoline
    Andres for pointing this out.

  • Added a logMessages global configuration variable that, if set to
    true, records messages on the JBrowse message bus in the browser
    log.

  • Added a workaround for problems with some types of nonstandard Perl
    installations. Thanks to Rebecca Boes for pointing this out.

About Robert Buels

JBrowse Lead Developer
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