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
We should use the structure for a variant as in the main API.  In particular, we should not use '-' in the reference 
sequence for an insertion, as proposed here.  Instead we should follow VCF in always requiring an explicit reference
base (or sequence of bases) to be replaced.  So deletion of T in ATC would be represented as replacement of "AT" by "A".
Then all operations are unambiguous string replacements.

Using an integer for zygosity, or copy number, is standard in some representations.  It is natural in association genetics, 
where it is called the allele dosage.

Richard

On 13 Sep 2014, at 19:08, Sergiu Dumitriu <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;
> Is this a widely accepted convention? I would find an enum better.
> 
> —
> Reply to this email directly or view it on GitHub.
> 




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