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
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
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