Add get methods for *sets

getReadGroupSet, getCallSet and getDataset
Allow searching for references by refSetId
Add variantSet.referenceSetId field
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.
Fixed error in variant location comments (position is of variant, not gene)
Merge remote-tracking branch 'upstream/master' into fix-variant-position-description
Merged in changes from PR #187
Merge pull request #191 from buske/fix-variant-position-description

Fixing error in comments. API unchanged.
case change GeneticSex

* changed case geneticSex => GeneticSex, to remain in format sync with other enum
* adapted the GeneticSex attribute for the Individual to be of enum format
Merge pull request #185 from mbaudis/master

Update of GASex to GeneticSex in metadata
Using a GAOntologyTerm for cell type rather than a string.
Using OntologyTerm rather than string from Cell Line

Note there may not be consensus on this. There are competitors in this
space, but the general schema should support any
Added link to Uberon
Added documentation for making an OntologyTerm for a taxon
making links markdown-friendly
making links (CL, CLO) markdown-friendly
removing obsolete GA prefix. See comments from @mbaudis on issue #164
Merge pull request #164 from cmungall/ontology

Use of ontologyTerm for cell types and cell lines