Adding scripts for publishing scaladoc.
Merge pull request #319 from fnothaft/publish-scaladoc

Adding scripts for publishing scaladoc.
Added the TrackedLayout class.
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.
Ran ./scripts/format-source