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:
- JBrowse-1.10.4.zip – 4.6M
file SHA1 0cfc8106e0b89fcc937701be74830c30b9f894cc
- JBrowse-1.10.4-dev.zip – 26M
file SHA1 9b4d7aa9c6cb702853e3080fd7dedfae32a095ca
- 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
- Added a CanvasVariants track type, similar to HTMLVariants, which
utilizes the faster CanvasFeatures rendering backend for displaying
- 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.
- 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