Would it be possible to make this component accept a 'sub-adaptor' for the fasta reference?
db_adaptor = Bio::DB::Sam
db_args = -bam /Library/WebServer/Documents/gbrowse2/databases/homosapiens/bam/PD2125b.bam
db_adaptor = Bio::DB::SeqFeature::Store
db_args = -adaptor DBI::mysql
search options = default
This has a two fold benefit if possible:
1. You only need to maintain the sequence in your DB rather than one on disk and one in the DB (especially useful if you will have multiple builds of the genome).
2. The DB should be faster, especially if you don't have local disk (e.g. virtual servers).