addReference() is a convenient method for create a fast way of comparing a Genotype with the reference, but an enhancement is remove this and create a "fake" genotype for the reference in tools that requires this comparison.
Like that we will suport imput a different reference, and we can name the reference in a different way and check if the pair is really a reference one. This also remove some unnecessary code complexity.
addReference()is a convenient method for create a fast way of comparing aGenotypewith the reference, but an enhancement is remove this and create a "fake" genotype for the reference in tools that requires this comparison.Like that we will suport imput a different reference, and we can name the reference in a different way and check if the pair is really a reference one. This also remove some unnecessary code complexity.