[ADAM-340] Adding the TrackedLayout trait and implementation.

OrderedTrackLayout is an implementation of TrackedLayout, which takes a sequence of Reference-mappable values and lays them out into tracks in a naive, order-dependent way.
Merge pull request #341 from genomebridge/tdanford/tracked-layout

[ADAM-340] Adding the TrackedLayout trait and implementation.
[ADAM-332] Upgrades ADAM to Spark 1.0.1.
Merge pull request #333 from fnothaft/upgrade-spark

[ADAM-332] Upgrades ADAM to Spark 1.0.1.
[ADAM-327] Adding Gene, Transcript, and Exon models