Simplify format-source

Only create a single Maven instance, and provide multiple goals to it
Merge pull request #279 from genomebridge/simplify-format-source

Simplify format-source
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