Adding in prePhase of Genome to accurately identify phase before and after
each denovo mutation
Partial support for Prephasing
adding Debug
Prephasing appears to be working properly, needs some testing before promotion to master
More work on prephasing
Limit Pedigree Search
Improvements to phasing code & support for recording depth information
cleanup
Merge branch 'prePhase'

Conflicts:
	advancedFilter.scala