add in an option to not report LOH calls
refactor: make method to evaluate if a combination of reference, tumor genotype and normal genotype should be filtered
Utilize, fix and test new function
update docs
update should_filter_as_loh logic:

previously, it would filter sites where the normal genotype was non-ref
and also a subset of the tumor genotype.

i think the intent was to filter sites where the tumor genotype differs
from the normal only by containing a ref allele.
add separate filter function for "gain of reference" filter
add gain of reference allele filtering as option
update docs for gain of reference allele filtering
add in -G option to getopt
fix -G option which apparently has been a non-functional option that expects a string since 2011
Merge pull request #3 from genome/no_loh

Merge in command line options for filtering LOH and GOR sites.