JBrowse 1.12.4 has been released, with a great many improvements and bugfixes! Apologies for the long delay since the last release.
One highlight of this release is that we have fixed a severe incompatibility that prevented many of the JBrowse formatting scripts from running correctly on Perl 5.18 and above.
However, there have been a HUGE number of smaller improvements and bugfixes, have a look at the release notes below!
Files for download
- JBrowse-1.12.4.zip – 5.7M
file SHA1 9c3b88d982ceb86de9999e49ddde631d6b41a28f
- JBrowse-1.12.4-dev.zip – 30M
file SHA1 bb3fa872cbc57055712114e3e01cdcad6776a3b6
- Fixed SEVERE performance regression that basically made flatfile-to-json.pl
unusable on Perl 5.18 and higher. Huge thanks to Colin Diesh for tracking
this down. (issue #470, issue #912, @cmdcolin)
- Added code to calculate feature density histograms for Tabix-indexed GFF3
GFF3Tabix) data sources. Thanks to @nathandunn for noticing and fixing
this! (issue #956, @nathandunn)
- Added a new “Hide unspliced reads” menu item to Alignments and Alignments2
tracks that filter out reads that have no
Ns in their CIGAR strings.
Thanks to Deepak Kunni and Nathan Dunn for their work on this.
(issue #921, @deepakunni3)
- setup.sh now uses npm instead of Bower (which is deprecated) to install
- Removed legacy
- Added a
prepare-refseqs.plto allow injecting
refseq configuration variables at format time. (issue #884, @erasche)
- Added trackLabels: “no-block” config feature. Moves track labels/menus
above the features so as not to obscure the features. (issue #901, #490)
- Added a
set the new track’s category. Thanks to @loraine-gueguen for the implementation!
(issue #911, @loraine-gueguen)
- Made jbrowse installable using
npm. @cmdcolin and @enuggetry.
- Implemented a built-in node.js Express server
jb_run.jsfor quick JBrowse launching.
- Added an
prepare-refseqs.plthat formats reference sequences
in the same order in which they appear in the input sequence file. Thanks to
@dsenalik for the suggestion and implementation! (issue #924, @dsenalik)
- Allows for dot-notation instead of JSON (issue #952) for addTracks, addBookmarks,
and addStores. https://github.com/GMOD/jbrowse/pull/952. Address security concerns
adding JSON to GET (https://nvd.nist.gov/vuln/detail/CVE-2016-6816) @nathandunn.
- If a track has no
keyset in its track configuration, JBrowse will now look for
keyin its track metadata, and use that if it is present. Thanks to Loraine
Guéguen for the idea (issue #957, issue #958). @rbuels
- Fixed bug in
maker2jbrowsescript that allows
maker2jbrowseto be installed
in system executable directories, and adds a
(issue #877, @cmdcolin)
- Fixed a cosmetic/styling bug with malformed DOM structure in feature detail popup
dialogs. Thanks to Erik Rasche for noticing and fixing this! (issue #882, @erasche)
- Added a configuration option that can disable JBrowse’s behavior of updating the
browser’s title text as the view changes. Thanks to Luka Jeran, Primož Hadalin,
and Nathan Dunn for this! (issue #904, @lukaw3d)
- Suppress execution of biodb-to-json.pl on sample data while running setup.sh
on MacOS High Sierra with stock Perl due to an issue with the stock Perl having
broken BerkeleyDB integration, which is needed by Bio::DB::SeqFeature::Store,
the main storage engine used by biodb-to-json.pl. Bug was manifesting as the script
running indefinitely and taking all available disk space.
(issue #945, issue #946, @deepakunni3 and @rbuels)
- Mitigate race condition that could sometimes cause duplicate tracks to be shown
when the browser is started with the
locquery parameeter set to the name of
a feature. Thanks to Colin Diesh for the fix. (issue #567, @cmdcolin)
- Fixed issue in which JBrowse crashed when negative numbers were supplied for highlight
coordinates in the URL. Thanks to @h2akim for reporting, and @cmdcolin for debugging help.
(issue #769, @rbuels)
--configcommand-line option to
scripts. Thanks to Chris Childers for suggesting this! (issue #620, @rbuels)
- Fixed a “cannot read property ‘offsetLeft'” error when using touch screens without
the old simple track selector active. (issue #893, @rbuels)
- Upgraded to use new Google Analytics API for usage reporting. (@rdhayes)
- Fixed bug in which start/stop codons were sometimes not displayed in the sequence
track at certain zoom levels (issue #858, pull req #859, @cmdcolin)
- Fixed a regression in which the
defaultTracksconfiguration variable was no longer
respected when set to a comma-separated list. (issue #892, issue #896, @rdhayes)
- Made a cosmetic change to Alignments track detail popups, changing “Length on ref” to
be displayed as “Seq length on ref”, so that it is displayed more usefully next to
“Seq length”. Thanks to @colindaven for the suggestion and implementation!
(issue #939, @colindaven)
- Improved the error messages displayed when a JBrowse glyph class fails to load. Thanks
to @scottcain and @cmdcolin for tracking down the issue and improving the error
handling! (issue #968, @cmdcolin)
- Added support for an
addFeaturesURL query parameter that can inject features from
the URL query string. (issue #976, @nathandunn)
- Changed the project’s
gitworkflow to utilize a
devbranch that is separate from
masteronly being updated when a new release of JBrowse is published.
(issue #975, @enuggetry)
- Implemented automated deployment of JBrowse releases to GitHub releases and
Thanks to @abretaud, @nathandunn, @erasche, and @cmdcolin for valuable discussions.
(issue #822, issue #979, issue #984, @rbuels)
- Added a
add-bam-track.plto support configuring pregenerated
coverage histograms from the command line. Thanks to @loraine-gueguen for the suggestion
and implementation! (issue #972, @loraine-gueguen)
- Improved documentation of the
CategoryURLplugin. (issue #985, @enuggetry)