Issue #173: Initial commit of MatchmakerExchange V1 API, as currently implemented in the wild.
Update variants.avdl

Standardize genotype likelihoods to log10(P(data | phenotype)), as in the VCF GL tag.
Merge pull request #174 from buske/master

Initial commit of MatchmakerExchange V1 API, as currently implemented in the wild.
Revert "Initial commit of MatchmakerExchange V1 API, as currently implemented in the wild."
Merge pull request #177 from ga4gh/revert-174-master

Revert "Initial commit of MatchmakerExchange V1 API, as currently implem...
Issue #173: Re-adding initial Matchmaker API without GA prefix
Initial PR #174 was reverted in #177 because GA prefixes were removed from project while PR was in review.
Add get methods for *sets

getReadGroupSet, getCallSet and getDataset
Allow searching for references by refSetId
Add variantSet.referenceSetId field
Merge pull request #179 from buske/master

Re-adding initial Matchmaker API without GA prefix
Declare properPlacement == SAM flag 0x2
Update of metadata.avdl

This is a re-edition of the metadata.avdl change regarding the GASex definition, competing with @cassiedoll's changes in https://github.com/ga4gh/schemas/pull/138 
It implements some of the ideas/wishes from the discussion there and adds addtl. fixes:

* type "OTHER"
* explanation of definition/use
* deletes the "NOT_AVAILABLE" type since base is NA => 'null'
* removes the "GA" prefix

However, the move to common is not implemented here & will be done later if enough agreement.
Update of metadata.avdl

This is a re-edition of the metadata.avdl change regarding the GASex definition, competing with @cassiedoll's changes in https://github.com/ga4gh/schemas/pull/138 
It implements some of the ideas/wishes from the discussion there and adds addtl. fixes:

* type "OTHER"
* explanation of definition/use
* deletes the "NOT_AVAILABLE" type since base is NA => 'null'
* removes the "GA" prefix

However, the move to common is not implemented here & will be done later if enough agreement.
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