ld_sub_geno () does not calculate the full linkage disequilibrium among a set of loci, it calculates a subset of it.  We can use the following recursive algorithm to calculate the right value (where U is the set of loci we're interested in, and |U| is its size):

1. If |U| = 0, or |U| = 1 then return 0
2. If |U| = 2 then use the standard linkage disequilibrium
3. If |U| > 2 then split off a locus and use the following formula

  E[X_i \Pi_{j \in U/i} (X_j - p_j) ] - p_i D_U/i

  with recursion on the last term.  U/i is the set difference of U and i, X_i is an indicator variable giving the status to the locus (on or off) and E represents expectation (genotypic average).

For each such calculation we will need the genotypic frequency (for averaging) and the allele frequencies of the constituent alleles (can be calculated once).