Reworking the formatting in variationReference.avdl to be more in line with the code style standards.
Merge branch 'master' of github.com:ga4gh/schemas into variationReference
Lining up comments slightly better
Update variants.avdl

Standardize genotype likelihoods to log10(P(data | phenotype)), as in the VCF GL tag.
Merge branch 'master' of github.com:ga4gh/schemas into variationReference

Now doesn't have the GA prefix.

Conflicts:
	src/main/resources/avro/wip/variationReference.avdl
Responding to comments from GitHub.
Add get methods for *sets

getReadGroupSet, getCallSet and getDataset
Allow searching for references by refSetId
Add variantSet.referenceSetId field
Declare properPlacement == SAM flag 0x2
Updated whitespace and "observed" status of features
Removed "/mmapi" prefix to endpoints, since this can be negotiated as part of the base_origin_url
[cleanup] Removed trailing whitespace from lines
Updated modeOfInheritance to use HPO term
Updated variant type to use Sequence Ontology term identifier
Moved the patient id into the Match object, so the response also include an identifier for the matching patients
Moved assembly to top-level instead of per-variant
Replaced gender with GA4GH representation of sex
Fixed error in variant location comments (position is of variant, not gene)
Merge pull request #175 from awblocker/master

Update variants.avdl