JBrowse 1.10.5 maintenance release

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.

Bug fixes

  • 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).

About Robert Buels

JBrowse Lead Developer
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