init GMM on clust and min_dist 0.5

also set min_var to 1e-5
there were issues where occassionaly the gmm fit would bring that wayyy
down for just one fit and then that particular fit woudl have an uber
high BIC because the var was way less
fix bug for the number of clusters

number of clusters variable in the GMM_gt object is incorrect because
it's based on the original params and which GMM was picked, however,
that GMM could have been pruned since then
fix genotyping of a single individual

in output single individuals were trying to be genotyped.
include indivs CAN be none
VCF filtering
force genome names to strings
add X-linked test filter
refactored return
add max_cp filter and +1 to fastahack
added some comments
target specific loci option added
added hel;ful. coments
merge correlated at lower cutoff in dups
print out correlated merge
aggressively cluster in dup regions
a simple plotting test
add singleton filter

make sure singletons are a specified distance (in SDs) from all the
other individuals
add additional filtering for duplicaions

add a min-sigma filter for duplications
np.max -> np.amax
added comments