First commit of the matchmaker APIs

This is a wip translation of the matchmaker APIs into avro.

Autogenerated docs are here: http://cassiedoll.github.io/matchmaker-staging.html
I really think that GA4GH should have a consistent representation for genetic variation.  Making a different representation in the MatchMaker interface
and the Variants interface would send a bad message of not being joined up.  I suggest that MatchMaker either use the Variant interface developed
by the Data Working Group, or at least uses a representation consistent with it.  Having '-' in the reference bases to represent an insertion is not 
consistent with the Variant interface, or with VCF, which Variant.avdl is based on and which has been a standard used for years.  I expect that all 
the tools that Orion mentions can already parse VCF, so it would not create confusion to use the VCF conventions - rather the reverse.

Richard

On 27 Sep 2014, at 00:39, Orion Buske <notifications@github.com> wrote:

> In src/main/resources/avro/wip/matchmaker.avdl:
> 
> > +  union { null, long } end = null;
> > +
> > +  /**
> > +  The reference bases. (e.g. `-`, `A`, `ACG`, …, where `-` is used to indicate
> > +  an insertion)
> > +  */
> > +  union { null, string } ref = null;
> > +
> > +  /**
> > +  The alternate bases. (e.g. `-`, `A`, `ACG`, …, where `-` is used to indicate
> > +  a deletion)
> > +  */
> > +  union { null, string } alt = null;
> > +
> > +  /** 1 for heterozygous or hemizygous, 2 for homozygous; */
> > +  union { null, int } zygosity = null;
> Though the allelic dosage is used in some contexts (and I'm actually the one who originally put this in the original API), I agree that using a VCF-style indexing into ref/alts might provide necessary flexibility down the line.
> 
> Also, Richard, I would actually be very hesitant to require prefix bases. Yes it requires the receiving system to actually have a copy of the reference genome to know the exact bases, but these prefix bases can lead to inconsistencies in the representation of indels, and in practice have to just be removed by database-based annotation tools anyway (e.g. CADD, Exomiser, SilVA, ANNOVAR, etc.).
> 
> —
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> 




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