change task depth count to use countbyvalue
drop val from PR feedback
Merge pull request #185 from hammerlab/improve-partition-counting

Change task depth count to use countbyvalue
dropping unused somatic calling code
Merge pull request #187 from hammerlab/code-drop

Dropping unused somatic calling code
drop duplicate overlaps function
Merge pull request #188 from hammerlab/dup-overlaps-func

Drop duplicate overlaps function
Clean up some logic in SomLogOdds caller

- simplify some of the list/option comprehending
- make normal/tumor code-paths more symmetric
better assert message in DistributedUtil

also fix a long line
apply reference base read quality to Deletions
add back check for tumor genotype being variant
limit to one variant per locus

only consider the first non-reference allele in the tumor genotype
long line
add a TODO