JBrowse 1.12.5 maintenance release

JBrowse 1.12.5 has been released!

Files for download

Minor improvements

  • Safari versions 10 and 11 will now see buttons for downloading feature FASTA
    sequences, as well as other sequences. These were turned off for all Safari
    browsers back when no version of Safari could download a client-generated file,
    but Safari 10 and 11 support it now. Thanks to @kkara for noticing the button
    was missing and prodding us to look into it. (issue #714, @rbuels)
  • Changed the default color for HTMLFeatures features to be a darker gray that
    is easier to see. Many thanks to @colindaven for the fix! (issue #980, @colindaven)
  • Added the ability to manually specify a reference sequence ordering in the
    configuration. Users can now set refSeqOrder: "by_list" and then set
    refSeqOrderList: "ctgX,ctgY,ctgZ" to manually specify an ordering.
    Thanks to @dsenalik, @liub1993, @wkpalan, and @cmdcolin for valuable
    discussions about this, and @rdhayes for the prototype implementation.
    (issue #867, issue #919, issue #1007, @rdhayes)
  • Added a --noSort option to prepare-refseqs.pl that preserves the reference
    sequence ordering in the input file, instead of sorting the reference sequences
    alphabetically in the JSON. Thanks to @dsenalik for the prototype implementation
    of this, and @cmdcolin and @rdhayes for valuable discussions.
    (issue #925, issue #924, issue #1007, @dsenalik)
  • Feature tracks now support a showNoteInAttributes flag that force the feature’s
    Notes attribute to be displayed as a regular attribute in the feature detail
    popup. This is to support the case in which users want the blue description text
    on a feature to be different from the feature’s Notes attribute, but still display
    the Notes attribute in the detail dialog. Thanks to @loraine-gueguen and @cmdcolin
    for the idea and the implementation. (issue #885, @cmdcolin)
  • When users click on an item in the dropdown autocompletion for the browser search
    box, the browser will go directly to that item immediately, eliminating the extra
    step of the user having to click “Go”. Many thanks to @enuggetry for noticing the
    opportunity for this nice usability enhancement! (issue #616, issue #1001, @rbuels)
  • The global highResolutionMode configuration is now set to auto, meaning that
    JBrowse by default will now auto-detect high-DPI displays (Apple Retina displays
    and similar) and draw canvas-based tracks more clearly on them. This capability
    has been present in the JBrowse code for a long time, but has been turned off
    by default. (@rbuels)
  • Added support for two new configuration variables for SNPCoverage tracks:
    indicatorProp and indicatorDepth, which set the minimum proportion (indicatorProp)
    and minimum depth (indicatorDepth) of alternative alleles required to render the
    SNP indicator below a SNPCoverage track. Big thanks to Nathan Haigh for the idea
    and implementation! (issue #951, @nathanhaigh)
  • Added a basic loading screen for when the page is initially loading (issue #1008,
  • The subfeatureDetailLevel configuration variable for tracks now defaults to a value
    of 2, meaning that the builtin JBrowse default feature detail popup dialogs will only
    show one level of subfeatures by default. Most feature tracks have only one level of
    subfeatures anyway, but for very complex data (like gene models with many transcripts,
    each with many introns and exons), this new default will prevent a rather confusing
    problem some users were seeing in which JBrowse would seem to ‘hang’ when clicking a
    gene model to see its details. Thanks to @cmdcolin for the original implementation of the
    subfeatureDetailLevel configuration variable, @kshefchek for a good bug report that
    shows it, and @nathandunn and @selewis for valuable discussions.
    (issue #559, issue #1010, @rbuels)

Bug fixes

  • Fixed a security issue with JBrowse error messages. Thanks to @GrainGenes for
    noticing and reporting it! (issue #602, @rbuels)
  • Fixed an off-by-one error in the “Next segment position” field of BAM features.
    Thanks to @keiranmraine for reporting it, and @rdhayes for tracking down the fix!
    (issue #907, issue #986, @rdhayes)
  • Fixed the broken demo track data source in the modENCODE sample data. Thanks
    to @cmdcolin for the fix! (issue #999, @cmdcolin)
  • Fixed bug in which dragging an Alignments or Alignments2 track into a combination
    track caused the combination track to crash. (issue #771, @cmdcolin)
  • Feature detail dialogs for variant tracks now correctly display “no-call” in
    the genotype details table for “./.” alleles. Thanks to @carrere for reporting
    it, and @cmdcolin for the fix. (issue #980, issue #990, @cmdcolin)
  • Fix parsing of the END field in VCF tracks, enabling things like CNV and deletion
    variants to be visualized from variant tracks. (issue #847, @cmdcolin)
  • Fixed a long-standing bug in JBrowse configuration template parsing that
    prevented use of dot-notation nested variable names, e.g. {foo.bar}, in
    JBrowse configuration, as well as whitespace inside the braces. Big thanks to
    @wuroger for finding this bug. (issue #1012, @rbuels)

About Robert Buels

JBrowse Lead Developer
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