/// <summary>
/// Return a VCF-like string representation for the alleles of this genotype.
///
/// If ignoreRefState is true, will not append the reference * marker on the alleles.
/// </summary>
/// <returns> a string representing the genotypes, or null if the type is unavailable. </returns>
public virtual string getGenotypeString(bool ignoreRefState)
{
if (Ploidy == 0)
{
return("NA");
}
// Notes:
// 1. Make sure to use the appropriate separator depending on whether the genotype is phased
// 2. If ignoreRefState is true, then we want just the bases of the Alleles (ignoring the '*' indicating a ref Allele)
// 3. So that everything is deterministic with regards to integration tests, we sort Alleles (when the genotype isn't phased, of course)
return(String.Join(Phased ? PHASED_ALLELE_SEPARATOR : UNPHASED_ALLELE_SEPARATOR, ignoreRefState ? AlleleStrings :
(Phased ? Alleles.Select(x => x.ToString()) : ParsingUtils.SortList(Alleles).Select(x => x.ToString()))));
}
/// <summary>
/// Returns how many times allele appears in this genotype object?
/// </summary>
/// <param name="allele"> </param>
/// <returns> a value >= 0 indicating how many times the allele occurred in this sample's genotype </returns>
public virtual int CountAlleles(Allele allele)
{
return(Alleles.Count(x => x.Equals(allele)));
}
private void AddGenes(IEnumerable <bool> genes)
{
Alleles.AddRange(genes);
}
public void AddGene(bool gene)
{
Alleles.Add(gene);
}