A new JBrowse release has arrived! JBrowse 1.11.5 incorporates many valuable contributions and feedback from the community which has been overwhelmingly positive. Some notable bugs have been fixed, including a long-standing VCF file parsing bug, a scrolling bug that affected popup boxes for variants on JBrowse 1.11.4, and a patch for setup.sh build errors. There are also some new configuration options for the tracklist and dialog boxes, and a bug that was preventing tablet and touch-screen devices from working was fixed!
The release can be downloaded from http://jbrowse.org/jbrowse-1-11-5
Full release notes:
## Minor improvements
* Added the ability to disable sorting on the Hierarchical track
selector using the sortHierarchical flag. Thanks to Chris Childers
for the suggestion and Colin Diesh for the implementation
* Added saving of the display mode setting on the CanvasFeature based
tracks. Thanks to Jon Hinton for the idea and Colin Diesh for the
fix (issue #469).
* Added configurable click event handlers for Wiggle type tracks.
Thanks to Richard Hayes for implementing this feature (issue #489).
* Added more configuration options for 'View details' popups as well
as the ability to customize the 'About track' popups. Thanks to
Colin Diesh for the idea and implementation (issue #494).
* Added the ability to load the category attribute from trackMetaData
files to be used for the Hierarchical track selector.
* Added the ability to specify initially collapsed categories in the
Hierarchical track selector (issue #507).
* Added beta touch-screen and tablet support by fixing a related bug.
Thanks to Paul Hale and Kieran Raine for reporting bugs and to
Emily Greenfest-Allen for the suggested fix (issue #505).
## Bug fixes
* Fixed a bug with VCF tabix file parsing that caused unnecessary
chunkSizeLimit errors. Thanks to Richard Hayes for finding and
debugging this issue (issue #486)!
* Fixed a bug where the Variant popup boxes would not display
complete genotype information in previous 1.11.* versions.
Thanks to Nando for reporting the bug and Colin Diesh for the
bugfix (issue #488).
* Fixed a small error that occured when using variant type tracks
with the REST API.
* Added a bugfix that caused problems scrolling in dialog boxes
for variant type tracks in 1.11.4 (issue #492).
* Fixed the use of the --refs flag on prepare-refseqs.pl. Thanks to
Audrey for finding & fixing this bug (issue #497).
* Added missing template length flag to the Alignments popup dialogs.
Thanks to Kieran Raine for the suggestion and Colin Diesh for the
fix (issue #471).
* Fixed the functionality of the --incremental flag in the
generate-names.pl script. Thanks to Richard Hayes and Colin Diesh
fixing the issue (issue #478).
* Fixed legacy bam-to-json.pl support when running setup.sh due to
samtools build modifications (issue #501).
University of Missouri, Columbia
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