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:
- JBrowse-1.11.3.zip – 4.7M
file SHA1 24a8ef5f43fc01b5992806a4991d846440bd08e9
- JBrowse-1.11.3-dev.zip – 26M
file SHA1 a74fb4c6dcc519877d7361a2158168aee6ca64f3
- 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
- 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
Alignments2tracks 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
*.density.*as histograms to newly-opened tracks if the file
basenames match. For example, if both
added as a histogram source for
mysample.bam. Thanks to Keiran
Raine and Alexander Stoddard for suggesting this (issue #423).
- 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)