* `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
## 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