Clean up callSampleId and Name fields

- make callSampleId on GACall optional
- remove callSampleIds and callSampleNames from GAVariantSet
- add a comment clarifying that if callSampleId is not on a GACall, the results from a /callsamples/search?variantSetIds=x will be returned in the same order as the calls on a variant in that set
(and so the ith result maps to the ith call)

This means we can support both sparse and dense representations without too many differences in the API.
Add method comment for call sample ordering
Add number of results comment.
Clean up comments
Make variant methods documentation friendly

- change the comments to the right style
- tie the request/response objects together like we did for readsets
Merge pull request #85 from cassiedoll/variant-methods

Make variant methods documentation friendly
callsample -> callset
callsample -> callset
fix callSet casing
fix callSet casing
Fix typo
Create variationReference.avdl

This is Richard's starting .avdl for representing a sequence graph.
position --> [start, end)
addition doc for end
Merge pull request #92 from massie/referenceVariationGraph

Add the variationReference data description
Merge pull request #79 from cassiedoll/callSampleIds

Clean up callSampleId and Name fields
Merge remote-tracking branch 'upstream/master' into callsample-callset

Conflicts:
	src/main/resources/avro/variants.avdl
Fix typo
Merge pull request #90 from cassiedoll/callsample-callset

Rename callSample -> callSet to match graph api
Merge pull request #93 from heuermh/position-to-start-end

Variant position --> [start, end)