JBrowse 1

JBrowse 1.10.4 maintenance release

September 23, 2013

JBrowse 1.10.4 has been released, with a new simple sequence-search track tool, large performance improvements for generate-names.pl, and some new filtering options for VCF-based variant tracks.

Files for download:

Minor improvements

  • Rewrote many parts of generate-names.pl, making heavy use of temporary BerkeleyDB stores (using Perl's DB_File module). This improves generate-names.pl performance by more than 10x.
  • Added a File->Add sequence search track menu item that can make tracks that show which regions of the reference sequence contain a given (small) sequence, or match a given regular expression. Thanks to Daniel Kasenberg for the initial implementation of this (issue #315).
  • Added a CanvasVariants track type, similar to HTMLVariants, which utilizes the faster CanvasFeatures rendering backend for displaying variant data.
  • Added checkboxes to HTMLVariants and CanvasVariants track menus that allow filtering displayed features based on the FILTER attribute in a VCF file. In addition to filtering based on the presence or absence of PASS, users can filter based on the custom filters defined in the VCF header. Thanks to Keiran Raine and Andrew Uzilov for suggesting this (issue #344).
  • Added "Hide forward strand" and "Hide reverse strand" checkboxes to Alignments and Alignments2 track menus that allow alignments on the forward and/or reverse strands to be hidden.

Bug fixes

  • Fixed a bug that prevented indexing of feature aliases in the names index when running generate-names.pl.
  • Fixed a bug that prevented proper display of the "ibeam" feature class in HTMLFeatures tracks. Thanks to Ed Lee for pointing this out.
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