change allele equality
adding tests for allele
Merge pull request #183 from hammerlab/allele-equality

Change allele equality
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