JBrowse 1.11.5 released

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JBrowse 1.11.5 released

Diesh, Colin M.
Hello everyone,

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
   (issue #477).

 * 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).


Happy browsing!

Colin Diesh
Research Analyst
Elsik Lab
University of Missouri, Columbia