Inconsistent genotype.count definitions

[d-cameron]

"The genotype.count attribute explicitly captures the total count of molecules associated with a genomic locus represented by the Genotype."

This definition is problematic when there are genomic rearrangements. For example, a tandem duplication will cause the duplicated region to be triploid so I would have assumed that I could use genotype.count=3 for SNVs and indels within this duplicated region. Unfortunately, the definition of genotype.count defines in terms of molecules thus genotype.count=2 is required since there's still only two relevant molecules for the tandem duplication. The defining table defines genotype.count in terms of abundance but the above-quoted clarifying text uses a different, inconsistent definition.

[github-actions[bot]]

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