Revert "rollback duplicate removal changes."

This reverts commit fa05115df99e5a3e2f3d8003efd0b9822fe6059d.
making loop over all variants in gene 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?