JBrowse 1

JBrowse 1.11.3 maintenance release

March 7, 2014

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)
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