Hi guys,

I was just looking at the FeatureDb class in GenomicFeatures. I'm wondering
if we couldn't abstract that from its SQLite implementation. There are many
other sources of features, e.g., files like BAM, VCF and even BED. If these
are indexed properly, we could make fast queries against them. So what we
really need is a class, named something like FeatureDb, that returns, for a
given 'which' (as a bare minimum), a GRanges.

I could also imagine having proxy FeatureDb objects that transform the data
on the way. Like a FeatureDb that will return the coverage, using another
FeatureDb as a source. Caching could be implemented as part of the base
class. I'm also wondering whether these should be reference classes. Then if
some "parent" FeatureDb is modified, the down-stream objects can be informed
of the change.

And a SequenceDb would be nice, too.

I'll write up a prototype in the MutableRanges package (in the bioc repo),
but I'll call it RangeDb to avoid conflicts for now.

Michael

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