Creating branch for redoing the ref/alt stuff will break things!
Also will work on PL/GL filtering when available.
Functional version?
Compile fixes
GATK Issues, due to missing AD
Still chasing Ad
Add PL check in when AD missing
Phred score to int
Require VCF type setting
Add basic phasing and phase reporting
More Phase Improvements
More Phase
Debug printing
more debug
Missing Conversion added
hide debug
Report from correct map
Try dif way of tracking child phase
bugfix
dito
Formating change