move more read count manipulation code into BreakDancer class
two changes:

Parse cmdline opts in Options() constructor rather than having a
parseArguments function that returns an Options struct.

Make do_break_func() equivalent to the similar code in Analysis to test
whether or not these two blocks can be deduplicated (signs point to
yes).
move most functions into BreakDancer class.

now we can work on splitting this class up