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[Bioc-devel] FeatureDb could be generalized

5 messages · Michael Lawrence, Marc Carlson

Original
Marc Carlson
# 
Hi Michael,

That is an interesting idea.  I like the idea of having more data be 
available via FeatureDb, and I especially like the idea of having useful 
transformations of the data it provides.  But I am a little confused 
about one part of what you are suggesting.  Is there a reason why we 
would want to add a bunch of stuff to basically re-implement what the 
database does instead of just writing some simple methods to allow the 
import of these other kinds to files?

I can think of advantages to keeping the data container type consistent 
(providing that it is not proving burdensome), since SQL allows joins to 
be made across databases thus allowing a collection of data that has all 
been stored in this way to be easily linked together as needed.  But 
what is the advantage of making a bunch of classes and methods that will 
allow us to pretend that our bam and vcf files are actually databases?

Also what would the purpose of a SequenceDb object be?  The name is 
generic enough that I am unable to guess what you have in mind.


   Marc
On 05/12/2011 06:08 AM, Michael Lawrence wrote: