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Experimental/alternative sequence stores

Marek Szuba requested to merge experimental/alternative_sequence_stores into master

Created by: andrewyatz

This code brings with it support for switchable adaptors. Might cause a merge conflict. Please merge #71 first.

The code has divided SequenceAdaptor into two objects.

  • SequenceAdaptor: communicates with the database to retrieve sequence
  • BaseSequenceAdaptor: has the ability to cache sequence in-between calls making the operation potentially more efficient

There are also some additional objects called FastaSequenceAdaptor and Faidx support. These are two example alternative stores. Faidx implements the indexing scheme from samtools/htslib to provide fast seekable access into FASTA files. The FastaSequenceAdaptor expects an instance of this object and delegates calls for sequence onto it.

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