Alphabetic genotype calls for allele states

[mtekman]

At the moment, expected genotype calls are {0,1,2, etc} to denote different alleles

Technically there is nothing wrong with using {A,B,C, etc} calls (other than limiting the number of alleles to < 26). These could be parsed to the default integer allele states upon file read without much re-write.

But is it right to? Again, this would limit the number of alleles. And would make Merlin's ambiguous call flag A almost indistinguishable from allele call "A".

[mtekman]

Partial fix for Merlin implemented in mapped branch