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
Merge pull request #184 from hammerlab/misc-somlogodds

Apply reference base read quality to Deletions
factor out moving over loci to an iterator to allow for folds
adding private modifier to sliding window iterator
adding tests for window fold
additional comments on SlidingWindowsIterator
approx read depth limits using the read data