Picking references when using update-db

[johnlees]

When running --update-db after --assign-query the sketches produced are inconsistent with the distances and the network.

I think this is because the reference is still randomly sampled from cliques rather than ensuring the previous reference is used when available. It's definitely desirable to avoid needing to resketch the original refs when updating both computationally and because it would mean the assemblies would need to be distributed with the database.

Need to update extractReferences() in network.py to use existing references from cliques where already defined.

[johnlees]

This may actually be a problem with inconsistent datasets/graphs, in which case this would be covered by #27

[johnlees]

Confirmed, this is a bug (previously had only tested with --full-db, I think)