genoprob_to_snpprob() doesn’t work for DOF1 cross type for X chr

[kbroman]

genoprob_to_snpprob() doesn’t work for DOF1 cross type for X chromosome. Currently it assumes that there are n choose 2 genotypes for females and n for males, but this is not tru for DOF1.

[kbroman]

The easiest solution would be to just pool the female and male genotypes on the X chromosome. Females are homozyg/heterozyg and males are hemizygous, but in the end there are just 8 genotypes.

[kbroman]

Converting the genotypes to allele dosages with genoprob_to_alleleprob() solves this problem. It doesn't do anything to the autosomes and for the X chromosome is simply place the male probabilities on top of those for females.