JBrowse-1.11.5 maintenance release

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 the ability to use tablet and touch-screen devices has been fixed!

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).
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