/// <summary>
/// Compute the end position for this VariantContext from the alleles themselves
///
/// In the trivial case this is a single BP event and end = start (open intervals)
/// In general the end is start + ref length - 1, handling the case where ref length == 0
/// However, if alleles contains a symbolic allele then we use endForSymbolicAllele in all cases
/// </summary>
/// <param name="alleles"> the list of alleles to consider. The reference allele must be the first one </param>
/// <param name="start"> the known start position of this event </param>
/// <param name="endForSymbolicAlleles"> the end position to use if any of the alleles is symbolic. Can be -1
/// if no is expected but will throw an error if one is found </param>
/// <returns> this builder </returns>
public static int ComputeEndFromAlleles(IList <Allele> alleles, int start, int endForSymbolicAlleles)
{
Allele reference = alleles [0];
if (reference.NonReference)
{
throw new Exception("computeEndFromAlleles requires first allele to be reference");
}
if (VariantContext.HasSymbolicAlleles(alleles))
{
if (endForSymbolicAlleles == -1)
{
throw new Exception("computeEndFromAlleles found a symbolic allele but endForSymbolicAlleles was provided");
}
return(endForSymbolicAlleles);
}
else
{
return(start + Math.Max(reference.Length - 1, 0));
}
}
