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);
}
/// <summary>
/// Get the number of values expected for this header field, given the properties of VariantContext vc
///
/// If the count is a fixed count, return that. For example, a field with size of 1 in the header returns 1
/// If the count is of type A, return vc.getNAlleles - 1
/// If the count is of type G, return the expected number of genotypes given the number of alleles in VC and the
/// max ploidy among all samples. Note that if the max ploidy of the VC is 0 (there's no GT information
/// at all, then implicitly assume diploid samples when computing G values.
/// If the count is UNBOUNDED return -1
/// </summary>
/// <param name="vc">
/// @return </param>
public virtual int getCount(VariantContext vc)
{
switch (countType)
{
case Bio.VCF.VCFHeaderLineCount.INTEGER:
return(count);
case Bio.VCF.VCFHeaderLineCount.UNBOUNDED:
return(-1);
case Bio.VCF.VCFHeaderLineCount.A:
return(vc.NAlleles - 1);
case Bio.VCF.VCFHeaderLineCount.G:
int ploidy = vc.GetMaxPloidy(2);
return(GenotypeLikelihoods.numLikelihoods(vc.NAlleles, ploidy));
default:
throw new VCFParsingError("Unknown count type: " + countType);
}
}
