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Commented exactly how the results are represented from the exact model so developers can know how to use them.

This commit is contained in:
Eric Banks 2011-12-19 10:19:00 -05:00
parent 3069a689fe
commit 5fd19ae734
1 changed files with 8 additions and 1 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/AlleleFrequencyCalculationResult.java
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@ -34,10 +34,17 @@ package org.broadinstitute.sting.gatk.walkers.genotyper;
*/ */
public class AlleleFrequencyCalculationResult { public class AlleleFrequencyCalculationResult {
// note that the cell at position zero in the likelihoods/posteriors array is actually probability of non-ref (since it's marginalized over all alleles) // IMPORTANT NOTE:
// These 2 arrays are intended to contain the likelihoods/posterior probabilities for each alternate allele over each possible frequency (from 0 to 2N).
// For any given alternate allele and frequency, the likelihoods are marginalized over values for all other alternate alleles. What this means is that
// the likelihoods at cell index zero (AF=0) in the array is actually that of the site's being polymorphic (because although this alternate allele may
// be at AF=0, it is marginalized over all other alternate alleles which are not necessarily at AF=0).
// In the bi-allelic case (where there are no other alternate alleles over which to marginalize),
// the value at cell index zero will be equal to AlleleFrequencyCalculationModel.VALUE_NOT_CALCULATED.
final double[][] log10AlleleFrequencyLikelihoods; final double[][] log10AlleleFrequencyLikelihoods;
final double[][] log10AlleleFrequencyPosteriors; final double[][] log10AlleleFrequencyPosteriors;
// These 2 variables are intended to contain the likelihood/posterior probability for the site's being monomorphic (i.e. AF=0 for all alternate alleles)
double log10LikelihoodOfAFzero = 0.0; double log10LikelihoodOfAFzero = 0.0;
double log10PosteriorOfAFzero = 0.0; double log10PosteriorOfAFzero = 0.0;