JBrowse 1

JBrowse 1.10.9 maintenance release

November 8, 2013

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.

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