Revert "make sure site2 doesn't go past the end of the array?"

This reverts commit ad93da4bbe9fc8f8ea3321ed3ba98cb8b1296f3b.
Revert "If the inner loop starts for index+1, seen isn't necesasry to track duplicate pairs"

This reverts commit 799145dc81f11b911ba3b16e17a910bf6d54e533.
Revert "making loop over all variants in gene more efficient"

This reverts commit c013639fc843e1d66f4ae32862084389422ebede.
make comp_het loops more efficient

I don't know Python but it seems to me that if you start looping for
each site i in the gene, the second inner loop doesn't need to start at
site 1, it can start at i+1?  Also, then you don't have check for
duplicate pairs