final Map<Haplotype,Allele> alleles = new HashMap<>(haplotypes.alleleCount());
final Random rnd = GenomeAnalysisEngine.getRandomGenerator();
final int sampleCount = samples.sampleCount();
final int alleleCount = haplotypes.alleleCount();
for (int i = 0; i < sampleCount; i++) {
final List<GATKSAMRecord> sampleReads = result.sampleReads(i);
final int readCount = sampleReads.size();
final ReadLikelihoods.Matrix<Haplotype> sampleLikelihoods = result.sampleMatrix(i);
for (int a = 0; a < alleleCount; a++)
for (int r = 0; r < readCount; r++)
sampleLikelihoods.set(a,r,-Math.abs(rnd.nextDouble()));