-- The current implementation of AFCalcResult contains a map from allele -> log10pNonRef. The only use of this field is to support the isPolymorphic function per allele. The call to this function looks like isPolymorphic(allele, QUAL). The QUAL is a phred-scaled threshold where you want to include alleles where the log10pNonRef >= QUAL (appropriately transformed). The problem is that when log10pNonRef is large, it quickly gets set to 0, while it's complementary log10pRef value has a meaningful log10 value. For example, if log10pRef = -100 (not an uncommonly large value), log10pNonRef = 0.0.
-- In order to preserve precision and allow us to more finally differentiate high QUAL from low QUAL (but still poly) sites we should store log10pRef values instead, and test that log10pRef <= threshold.
-- See https://jira.broadinstitute.org/browse/GSA-671 for more information.
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