JBrowse 1.10.5 maintenance release

October 3, 2013

JBrowse 1.10.5 has been released, with some important bug fixes and more performance improvements for data formatting scripts.

Files for download:

Minor improvements

Greatly improved the speed and reduced the memory footprint when running prepare-refseqs.pl with the --fasta and --gff options.
Added an impliedUTRs option to the ProcessedTranscript and Gene glyphs for CanvasFeatures tracks. Thanks to Ben Booth for pointing out the need for this (issue #348).
Upgraded flatfile-to-json.pl to use a new version of Bio::GFF3::LowLevel::Parser for GFF3 parser, which has a lookback buffer limit that makes it easier to parse large GFF3 files that do not contain enough '###' directives.
Further improved the memory footprint and speed of generate-names.pl. Thanks to Richard Hayes for his continued help with testing improvements and reporting problems.
Removed explicit dependency on GD::Image, which is only used by the old tiled-image generation demo code. This will make dependency installation easier for many people, at a (very) small cost to backward compatibility.

Fixed a bad bug that prevented combination tracks from working. Thanks to Harry Yoo for pointing this out (issue #351).
Fixed a bug in which one of the temporary files used by generate-names.pl was not being created in the correct location. Thanks to Richard Hayes for testing this.
Fixed a bug in which generate-names.pl could sometimes crash when run with the -v (verbose) switch, or in setup.sh.
Fixed odd behavior when entering coordinate ranges in the location box under Safari. Thanks to Keiran Raine for pointing this out (issue #341).