Can variable `ld_prune_index_to_drop ` be implimented as a boolean array 

This variable is currently an array of integer array of dimension "variant_indexes". If it could instead be treated as a boolean array of with dimension "variants" the unique dimension would be avoided. As mentioned in https://github.com/pystatgen/sgkit/pull/913#issuecomment-1261958057 this is performance sensitive code and avoiding a unique dimension would not be worth an efficiency loss.