a) Genotype given alleles with indels
b) Genotyping and computing likelihoods of multi-allelic sites.
When GGA option is enabled, indels will be called on regular pileups, not on extended pileups (extended pileups will be removed shortly in a next iteration). As a result, likelihood computation is suboptimal since we can't see reads that start with an insertion right after a position, and hence quality of some insertions is removed and we could be missing a few marginal calls, but it makes everything else much simpler.
For multiallelic sites, we currently can't call them in discovery mode but we can genotype them and compute/report full PL's on them (annotation support comes in next commit). There are several suboptimal approximations made in exact model to compute this. Ideally, joint likelihood Pr(Data | AC1=i,AC2=j..) should be computed but this is hard. Instead, marginal likelihoods are computed Pr(Data | ACi=k) for all i,k, and QUAL is based on highest likelihood allele.
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