We are happy to announce JBrowse 1.12.3 release!
This release includes a lot of improvements and bugfixes and we thank the community for the support. Some great new features include parsers for new file formats including 2bit format, which can be loaded via prepare-refseqs.pl. There are also new parsers for tabix BED files, tabix GFF and IonTorrent BAM files. Some other improvements include a new `noFill` option to display BigWig tracks as a scatter plot, the `cacheMismatches` option that improves performance for BAM files with long reads, and many other small improvements and fixes.
In addition, visit the JBrowse Plugin Registry for a collection of great plugins.
JBrowse (Release) (4170 downloads)
file SHA1 a82b308fe22062c2144efed749e7633c3eeee10a
JBrowse (Release-Dev) (737 downloads)
– 28MB (development)
file SHA1 e5eda1fe148ed0e5501f31a95f34f77f4f9bd783
- Docker Image
JBrowse (OSX Desktop 64bit) (1527 downloads)
– 69M (OSX 64bit)
file SHA1 27eede348c613837b6b0a0cf91ee0ca5557d693b
JBrowse (Desktop Win) (1560 downloads)
– 61M (Windows 32bit)
file SHA1 14a8c9a870864462a96d6f52504556e76541e889
- Upgraded build system to install dependencies with bower and
updated to dojo 1.9.8 (issue #718).
- Added the ability to load tabix indexed GFF and BED files.
Thanks to Colin Diesh and @zhjilin for contributing (issue #670).
- Added ability to open BED files in the “Open track” user interface
- Added ability to access SPARQL and other jbrowse data stores via
CORS. Thanks to the WebApollo hackathon and Eric Rasche for
contributing (issue #679).
- Added extra coloring schemes for the Sequence track when using
protein residues. Thanks to Eric Rasche for the idea and
implementation (issue #673).
- Added ability to specify custom exporter classes for the “Save
track data” option, for example, adding exporter code in plugins
- Added ability to specify custom name store classes via plugins,
which allows plugins to implement their own search functionality
- Added a timeout for the track feature density calculations which
can aid problems like consistent chunkSizeLimit issues
(issue #540, issue #730).
- Added an option to specify multiple highlights, or bookmarks,
using the config file, a remote service, or the URL bar
- Added support for parsing BAM files from IonTorrent (issue #782,
- Added support for native file access to .2bit files (issue #759).
- Added list of plugins in about box (issue #848).
- Added cacheMismatches option to improve performance when viewing
long-read alignments (issue #860).
- Added subfeatureDetailLevel config item to make View details box
only load subfeatures on demand (issue #861).
- Added ability to draw scatter plot from BigWig tracks. Thanks to
Keiran Raine for the contribution (issue #741).
- Added a fullviewlink option for the URL bar to disable “View full
link” attribute in embedded JBrowse. Thanks to Vivek Krishnakumar
for contributing (issue #813).
- Added URL parameter &tracklabels=0 and config parameter to hide
track labels (issue #869).
- Added renderAlignment option which creates a per-base alignment
view of the read versus the reference (issue #795).
- Added inferCdsParts option which creates CDS subfeatures from a
continuous CDS region for CanvasFeatures glyphs. Thanks to
Vivek Krishnakumar for the contribution (issue #872).
- Added events tracks/focus, tracks/unfocus, allowing for context
switching based on selected track.
- Made the menu bar widgets centered again (issue #680).
- Fixed error where the sequence track would not load after “Open
sequence file” (issue #831).
- Fixed problem with persistant “Error reading from name store”
message. Thanks to Anthony Bretaudeau for contributing the fix!
- Reverted to standard eukaryotic codon set.
- Fixed issue where saving session in JBrowse Desktop where plugins
were not saved with session.
- Fixed an error if there were numerical values being used as label
or description for the CanvasFeatures type tracks. Thanks to
Eric Rasche for reporting (issue #673).
- Fixed some issues where the Gene glyph would not layout some
features correctly. Thanks to Eric Rasche for reporting
- Fixed an issue with JBrowse Desktop where saving session would not
save the tracks that were not visible.
- Added fix when using indexed fasta from prepare-refseqs.pl.
Thanks to @billzt for the report (issue #719).
- Added a fix for an issue where editing the configuration of files
that were opened by a user didn’t work. Thanks to @lpryszcz for
the report (issue #569).
- Fixed some inconsistencies where “Open sequence” on file with a
.fasta file extension failed (issue #696).
- Fixed issue where track labels would re-appear during scroll
- Added handler for click scrolling in genome view. Thanks to
@exogenesys for fixing (issue #709).
- Fixed a rare error that only affected some versions of Chrome
- Removed linear gradients from some NeatFeatures tracks
- Fixed issue where saving GFF3 would fail if the source data
was in VCF format (issue #800).
- Fixed issue where there was a mix of plugin declarations