e6d23a5129d57ddbf57fa685fda1591ea389c8d9,public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidExactAFCalculation.java,DiploidExactAFCalculation,computeLog10PNonRef,#VariantContext#number[]#AlleleFrequencyCalculationResult#,59
Before Change
public void computeLog10PNonRef(final VariantContext vc,
final double[] log10AlleleFrequencyPriors,
final AlleleFrequencyCalculationResult result) {
linearExactMultiAllelic(vc.getGenotypes(), vc.getNAlleles() - 1, log10AlleleFrequencyPriors, result);
}
@Override
After Change
final double[] log10AlleleFrequencyPriors,
final AlleleFrequencyCalculationResult result) {
final int numAlternateAlleles = vc.getNAlleles() - 1;
final ArrayList<double[]> genotypeLikelihoods = getGLs(vc.getGenotypes());
final int numSamples = genotypeLikelihoods.size()-1;
final int numChr = 2*numSamples;