two methods for Genotype: HasRefAllele HasAltAllele

[lindenb]

Description

I wrote two new functions for Genotype : hasAltAllele and testHasRefAllele because I often need to detect whether an ALT allele (or a REF) is present in a Genotype whatever is the genotype ploidy

I also copied a javadoc from SimpleAllele to Allele.

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[lbergelson]

@lindenb This looks good to me. Thank you.

[lbergelson]

Good call. This method is very confusingly named.