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
Merge pull request #184 from hammerlab/misc-somlogodds

Apply reference base read quality to Deletions