/// <summary>
/// parses the INFO fields for SV-specific information
/// </summary>
private StructuralVariant ParseSvFields()
{
// update each alternate allele
var sv = new StructuralVariant(VcfColumns, VcfReferenceBegin, VcfReferenceEnd, _renamer, _vid);
foreach (var altAllele in AlternateAlleles)
{
sv.AssignVariantType(altAllele, AlleleTrimmer);
}
return(sv);
}
// constructor
public VariantAlternateAllele(int begin, int end, string refAllele, string altAllele, int genotypeIndex = 1)
{
Start = begin;
End = end;
AlternateAllele = altAllele.ToUpperInvariant();
ReferenceAllele = refAllele.ToUpperInvariant();
GenotypeIndex = genotypeIndex;
int dummyInt = Start;
SuppAltAllele = SupplementaryAnnotationUtilities.GetReducedAlleles(dummyInt, ReferenceAllele, AlternateAllele).Item3;
IsSymbolicAllele = StructuralVariant.IsSymbolicAllele(altAllele);
CustomIntervals = new List <ICustomInterval>();
}