[ADAM-335] Updated README.md to reflect migration to appassembler.
Merge pull request #337 from fnothaft/appassembler-update-docs

[ADAM-335] Updated README.md to reflect migration to appassembler.
[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.
Added filterByOverlappingRegion to AdamRDDFunctions
Added the VizReads tool to CLI.

VizReads is a tool for interactive or static visualization of aligned reads along the genome.