JBrowse 1.10.9 maintenance release

JBrowse 1.10.9 has been released, with new incremental-updating support in generate-names.pl, along with some other bug fixes and small improvements.

Files for download:

Minor improvements

  • generate-names.pl now supports a --incremental or -i option
    that adds names to an existing index. Thanks to Richard Hayes for
    reminding me that this wasn’t done yet (issue #373).

  • Added a lower-performance, but more backward-compatible indexing
    backend to generate-names.pl that can be activated by passing the
    --safeMode command-line argument. The recent performance
    improvements to generate-names.pl have apparently tickled some bugs
    that are present in some installations. Thanks to Josie Reinhardt
    and GitHub user raj76 for their continued help troubleshooting
    this. If you find that name indexing is not working correctly, try
    running it again with --safeMode, and report to the mailing list
    if it helps.

  • Added support for using the JBrowse in-memory GFF3 adaptor to
    display web-accessible GFF3 files directly. See
    docs/tutorial/data_files/volvox.gff3.conf for an example
    configuration. Thanks to David Goodstein and Richard Hayes for
    motivating this.

Bug fixes

  • flatfile-to-json.pl now depends on the latest
    Bio::GFF3::LowLevel::Parser 1.8, which fixes a bug in which
    features with no ID, Parent, or Derives_from attributes were not
    being included in parsed data. Thanks to Gwendoline Andres for
    pointing this out.

  • Tweak BioPerl-handling code in biodb-to-json.pl to hopefully work
    better with BioSQL backends. Thanks to Brian Osborne for pointing
    this out.

About Robert Buels

JBrowse Lead Developer
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