[Bioperl-l] Bio::DB::Fasta changes

[Fields, Christopher J]

There have been a number of significant changes to Bio::DB::Fasta recently that haven't been discussed on the bioperl list.  In particular, much of the code has been moved to Bio::DB::IndexedBase.  At the moment some of these changes are breaking compatibility with other tools (namely MAKER, see: https://redmine.open-bio.org/issues/3389).  In the latter case I would consider this a significant API change that needs to be addressed.

Generally, whenever we make significant changes to modules these should always be run on a branch first (see recent changes to Bio::Tree), and we should at least discuss this on-list prior to merging with master.  I do think we should start that discussion now and decide what to do, e.g. roll back changes and push these to a branch, allow these to stay in master with revisions, etc.

chris