Update likelihood code to handle non-uniform allelic mixtures #571
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| lazy val uniqueAllelesCount = alleles.toSet.size | ||
| assume(alleleMixture.values.sum <= 1, "Allele fractions are larger than 1") |
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Will alleleMixture contain a reference allele so that we'd expect the sum to be ≈1?
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Yes, this test was originally = 1 but was thinking it might be more likely that we assume .5 for the reference and then something like .2 for the variant if it is a low purity sample. Could possibly come back and adjust this.
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gotcha… I feel like the existence of this runtime-check raises more questions than it answers; is this a failure mode we're worried about? I'm ok leaving it in but maybe add a comment explaining the thinking, it's a peculiar and somewhat unnerving thing to feel the need to assert!
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Hm ok, maybe to clarify - the mixture should be a true mixture where the weights sum to 1. The reason for the check is to ensure that the entered values are at least fractions ... will add some comments around this
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lgtm modulo adding a comment per above, and also some tweaks I sent in #574, which you can incorporate here or which I can pull out as a separate PR, uty! |
- private-ize a few methods - simplify alignment-inclusion API in likelihood calculation: simple boolean instead of arbitrary function - remove "Likelihood." from call-sites - misc line-spacing
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This PR contains the following changes:
Genotypefrom a collection of alleles to a map ofAllele-> Allele FractionLikelihood.scalaandLikelihoodSuite.scalato handle thisThis change is