Variation Reference Methods
Adding a draft of some methods for the variation reference methods. There's a lot of work to do to sync up the representations of samples with the current variants API.
Substantially revising variationReference.avdl to mirror some of the newer stuff from the Variants and References APIs. Not yet updating the methods.
First pass at updating the methods
Adding dataset enumeration and improving some comments.
Adding Back Alleles and Segments

After talking with Benedict, it makes sense to me what these are for and why we need them. We need to be able to make calls on portions of variants, so we can call the bit of a variant between two other variants on it, for example.
And if we can do that, we really ought to be able to call several of these Segments at once as one Allele (or so Benedict says). And then we ought to be able to call both ends of, say, an inversion together as one Allele, without reading through the whole thing.

And then we need the Scaffolds back to read through individual Alleles and not multi-Allele-at-once Calls. Abd they need to be associated with call sets and variant sets.
Merge branch 'graph' of github.com:ga4gh/schemas into variationReferenceMethods
Drafting graph conversion of normal schemas
Re-arranging changes to try and make the diff against the existing API definitions look nicer.
Adding back in reference names
Making Segments and Paths part of common.avdl
Alleles now use Paths, and we have only one definition of Segment
Changing back to Variants in the variants API, instead of Alleles
Fixing variant methods to talk about variant scaffolds.
Adding a GraphAlignment, and making it clear when to use it versus when to use a chimeric alignment as SAM would describe it versus when to use both