JBrowse 1.10.5 has been released, with some important bug fixes and more performance improvements for data formatting scripts.
Files for download:
- JBrowse-1.10.5.zip - 4.6M file SHA1 17a07058a98900d2cff5d1db441ab3d2b5a425a1
- JBrowse-1.10.5-dev.zip - 26M file SHA1 c060c487fcd361cc4b41075696cef6cfc005f150
Greatly improved the speed and reduced the memory footprint when running
prepare-refseqs.plwith the --fasta and --gff options.
impliedUTRsoption 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.plcould 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).