Merge pull request #263 from genomebridge/tdanford/referenceLengthFromCigar

Added AdamContext.referenceLengthFromCigar
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.
Fixed problems with rebase.