Preparation.hap.perm: Prepare for the haplotype permutation
In RVPedigree: Methods for Family-Based Rare-Variant Genetic Association Tests

This functions prepares for running the perm.hap function. The output of this function can be passed to that one.

1 2	Preparation.hap.perm(pedigree, generation.id, indices.haplotypes1, indices.haplotypes2)

`pedigree`	data frame with pedigree information in linkage format (four columns: family ID, individual ID, father ID, mother ID). For example the first for columns of a Plink `.ped` file or a Plink `.bim` file.
`generation.id`	a vector of length(sample size) which indicates if the subject is founder (`generation.id=0`), a child from first generation (`generation.id=1`), a child from second generation (`generation.id=2`), etc. This vector can be calculated by the `kinship2::kindepth()` function.