Modifying conversion code to resolve #112.
Merge pull request #260 from fnothaft/sanity-check-flags

Modifying conversion code to resolve #112.
Added RichADAMRecord.referenceLengthFromCigar

Computes the length of a read against the reference sequence, using a regex
on the CIGAR string.
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.