Completed todo item: for sites like
(eval)
20 12345 A C
20 12345 A AC
(comp)
20 12345 A C
20 12345 A ACCC
the records will be matched by the presence of a non-empty intersection of alleles. Any leftover records are then paired with an empty variant context (as though the call was unique). This has one somewhat counterintuitive feature, which is that normally
(eval)
20 12345 A AC
(comp)
20 12345 A ACCC
would be classified as 'ALLELES_DO_NOT_MATCH' (and not counted in genotype tables), in the presence of the SNP, they're counted as EVAL_ONLY and TRUTH_ONLY respectively.
+ integration test
327169b283