JBrowse 1.11.3 maintenance release

JBrowse 1.11.3 has been released, with quite a few improvements and bugfixes, including a new coloring scheme for BAM alignment tracks (Alignments2 tracks), a fix for some annoying bugs with the feature arrowheads, and some nice new configuration variables for customizing the display of certain fields in the default feature detail popup dialog boxes (see the JBrowse Configuration Guide for details).

In addition, this will be my last JBrowse release in my position as JBrowse lead developer.  Thank you all for the past two years of development; we’ve made some exciting strides, and it’s been great!

Files for download:

Minor improvements

  • Added a “Zoom to this” item in the default right-click menus for
    canvas-based feature tracks. Thanks to Paul Hale for the initial
    implementation of this.
  • Allow the user to set the document.domain property via jbrowse.conf
    which can be helpful especially if jbrowse is embedded in a iframe.
    Thanks to Kieran Raine for the idea and Colin Diesh for the bugfix
    (issue #440)
  • Improved the graphic design of the “Add sequence search” dialog box
    to make it clearer how to switch between providing an amino acid
    and a nucleotide sequence. Thanks to Kevin Mohamed for the initial
    implementation of this (issue #436).
  • Expanded the default color set of Alignments2 tracks to show
    different shades of color indications of reads with missing mate
    pairs, improperly aligned reads, and reads with mate pairs on
    different reference sequences. Thanks to Keiran Raine for
    implementing this (issue #443).
  • Added support to customize specific parts of the ‘View details’
    popups using callback functions. Thanks to Kieran Raine for the
    idea and Colin Diesh for the implementation (issue #421).
  • The File->Open tool will now can add files named *.coverage.* or
    *.density.* as histograms to newly-opened tracks if the file
    basenames match. For example, if both mysample.bam and
    mysample.coverage.bw are present, mysample.coverage.bw will be
    added as a histogram source for mysample.bam. Thanks to Keiran
    Raine and Alexander Stoddard for suggesting this (issue #423).

Bug fixes

  • Fixed a problem where the feature arrowhead would get stuck in the
    middle of the screen at high zoom levels. Thanks to Colin Diesh for
    the fix (issue #449).
  • Disabled the FASTA download button in the “View details” page on
    Safari (issue #412). This feature can’t be supported in Safari at
    this time, but it is still supported in most other browsers. Rob
    Buels and Colin Diesh contributed fixes to this issue.
  • Fixed a bug in the client-side GFF3 parser pointed out by Andrew
    Warren. Thanks Andrew! (issue #452).
  • Fixed the problem of translation frames being switched around at
    different zoom levels. Thanks to Kieron Taylor for the bug report
    and Colin Diesh for the bugfix (issue #435)
  • Fixed a bug where gene features in GFF tracks would not have
    arrowhead markers. Thanks to Colin Diesh for finding and fixing
    this issue (issue #454)

About Robert Buels

JBrowse Lead Developer
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