private static void computeLofK(
final ExactACset set,
final List<double[]> genotypeLikelihoods,
final double[] log10AlleleFrequencyPriors,
final StateTracker stateTracker) {
set.getLog10Likelihoods()[0] = 0.0; // the zero case
final int totalK = set.getACsum();
// special case for k = 0 over all k
if (totalK == 0) {
for (int j = 1; j < set.getLog10Likelihoods().length; j++) {
set.getLog10Likelihoods()[j] =
set.getLog10Likelihoods()[j - 1] + genotypeLikelihoods.get(j)[HOM_REF_INDEX];
}
final double log10Lof0 = set.getLog10Likelihoods()[set.getLog10Likelihoods().length - 1];
stateTracker.setLog10LikelihoodOfAFzero(log10Lof0);
stateTracker.setLog10PosteriorOfAFzero(log10Lof0 + log10AlleleFrequencyPriors[0]);
return;
}
// if we got here, then k > 0 for at least one k.
// the non-AA possible conformations were already dealt with by pushes from dependent sets;
// now deal with the AA case (which depends on previous cells in this column) and then update
// the L(j,k) value
for (int j = 1; j < set.getLog10Likelihoods().length; j++) {
if (totalK < 2 * j - 1) {
final double[] gl = genotypeLikelihoods.get(j);
final double conformationValue =
MathUtils.log10(2 * j - totalK)
+ MathUtils.log10(2 * j - totalK - 1)
+ set.getLog10Likelihoods()[j - 1]
+ gl[HOM_REF_INDEX];
set.getLog10Likelihoods()[j] =
MathUtils.approximateLog10SumLog10(set.getLog10Likelihoods()[j], conformationValue);
}
final double logDenominator = MathUtils.log10(2 * j) + MathUtils.log10(2 * j - 1);
set.getLog10Likelihoods()[j] = set.getLog10Likelihoods()[j] - logDenominator;
}
double log10LofK = set.getLog10Likelihoods()[set.getLog10Likelihoods().length - 1];
// update the MLE if necessary
stateTracker.updateMLEifNeeded(log10LofK, set.getACcounts().getCounts());
// apply the priors over each alternate allele
for (final int ACcount : set.getACcounts().getCounts()) {
if (ACcount > 0) {
log10LofK += log10AlleleFrequencyPriors[ACcount];
}
}
stateTracker.updateMAPifNeeded(log10LofK, set.getACcounts().getCounts());
}
