split a bit of read/region tracking out of BreakDancer class

into the new ReadRegionData class. The idea is to reduce the public
interface to this new class to the absolute minimum so we can focus on
refining the way breakdancer deals with reads and regions.
push more work into ReadRegionData class
move implementation of ReadRegionData fns outside of class body
Merge branch 'merged' into config
changes to start to hook things up. horrible.
more changes to start to hook things up. even more horrible.
compiling. may not be functional. tests are broken.
fixed some out of bounds errors. tests now pass