JBrowse 1.10.7 maintenance release

October 15, 2013

JBrowse 1.10.7 has been released, with some important bug fixes and added support for displaying feature density histograms from REST stores.

Files for download:

Minor improvements

Added an optional stats/regionFeatureDensities endpoint to the REST API that makes it possible to provide binned feature counts that HTMLFeatures tracks can use to display feature histograms. Thanks to Stuart Watt and Daniel Troesser for pointing out the need for this (issue #365).

Fixed a bad bug introduced in 1.10.6 in which FASTA files with line lengths longer than the configured chunk size were not correctly formatted. Thanks to Jean-Jack Riethoven for pointing this out (issue #363).
Fixed a bug introduced in 1.10.6 in which prepare-refseqs.pl would not respect the --noseq command-line option when using --fasta.
Fixed bug in which name or seq_id attributes are required for reference sequence features. Thanks to Daniel Troesser for pointing this out.
Fixed a bug that may have prevented some types of VCF files from being displayed (error message referring to inheritedFilters).
Fixed a bug in which "Zoom in to see feature" in Sequence tracks would wrap downwards below track at some zoom levels and window widths.
Fixed an off-by-one error in UTR attributes manufactured by the impliedUTRs mechanism of the ProcessedTranscript glyph. Thanks to Ben Booth for pointing this out (issue #362).
Fixed a bug in which score attributes of features were not being recorded by biodb-to-json.pl. Thanks to HongKee Moon for pointing this out (issue #364).
Removed a stray use of Carp::Always in GFF3-processing Perl code that may have caused problems in some installations.