Dropped filterLociWhoseContigsHaveNoRegions

Dropped filterLociWhoseContigsHaveNoRegions - this is useful if 1) the user misspecifies loci by including loci not in the file or 2) loci are not specified and the sequence dictionary has more sequences than actually in the file. These are easily solved by the user either specifying loci or using the flag to get loci from reads instead of the sequence dictionary. Otherwise has ~4-5min overhead on every run. Closes #140