JBrowse 1

JBrowse 1.12.4 maintenance release

February 14, 2018

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

Minor improvements

  • 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 dependencies. @enuggetry
  • Removed legacy wig-to-json.pl and bam-to-json.pl scripts. @rbuels
  • Added a --trackConfig option to prepare-refseqs.pl to 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 --category option to add-bw-track.pl and add-bam-track.pl to 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.js for quick JBrowse launching. @enuggetry
  • Added an --unsorted option to prepare-refseqs.pl that 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 key set in its track configuration, JBrowse will now look for a key in 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 maker2jbrowse script that allows maker2jbrowse to be installed in system executable directories, and adds a --sortMem option. (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 loc query 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)
  • Add --config command-line option to add-bw-track.pl and add-bam-track.pl 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 defaultTracks configuration 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 addFeatures URL query parameter that can inject features from the URL query string. (issue #976, @nathandunn)
  • Changed the project's git workflow to utilize a dev branch that is separate from master, with master only being updated when a new release of JBrowse is published. (issue #975, @enuggetry)
  • Implemented automated deployment of JBrowse releases to GitHub releases and npm. Thanks to @abretaud, @nathandunn, @erasche, and @cmdcolin for valuable discussions. (issue #822, issue #979, issue #984, @rbuels)
  • Added a --bigwigCoverage option to add-bam-track.pl to 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 CategoryURL plugin. (issue #985, @enuggetry)
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