private static GenotypeLikelihoodsAllelePair[] calculatePLcache(int altAlleles)
{
int numLikelihoods = GenotypeLikelihoods.numLikelihoods(1 + altAlleles, 2);
GenotypeLikelihoodsAllelePair[] cache = new GenotypeLikelihoodsAllelePair[numLikelihoods];
// for all possible combinations of 2 alleles
for (int allele1 = 0; allele1 <= altAlleles; allele1++)
{
for (int allele2 = allele1; allele2 <= altAlleles; allele2++)
{
cache[calculatePLindex(allele1, allele2)] = new GenotypeLikelihoodsAllelePair(allele1, allele2);
}
}
// a bit of sanity checking
for (int i = 0; i < cache.Length; i++)
{
if (cache[i] == null)
{
throw new Exception("BUG: cache entry " + i + " is unexpected null");
}
}
return(cache);
}
private static GenotypeLikelihoodsAllelePair[] calculatePLcache(int altAlleles)
{
int numLikelihoods = GenotypeLikelihoods.numLikelihoods(1 + altAlleles, 2);
GenotypeLikelihoodsAllelePair[] cache = new GenotypeLikelihoodsAllelePair[numLikelihoods];
// for all possible combinations of 2 alleles
for (int allele1 = 0; allele1 <= altAlleles; allele1++)
{
for (int allele2 = allele1; allele2 <= altAlleles; allele2++)
{
cache[calculatePLindex(allele1, allele2)] = new GenotypeLikelihoodsAllelePair(allele1, allele2);
}
}
// a bit of sanity checking
for (int i = 0; i < cache.Length; i++)
{
if (cache[i] == null)
{
throw new Exception("BUG: cache entry " + i + " is unexpected null");
}
}
return cache;
}