public void AssignAlternateAlleles()
{
// sanity check: skip reference sites
if (IsReference)
{
var infoEnd = ExtractInfoEnd();
if (infoEnd != null)
{
VcfReferenceEnd = (int)infoEnd;
}
IsSingletonRefSite = VcfReferenceEnd == VcfReferenceBegin || VcfReferenceEnd == -1;
// basic blank allele for ref sites
var refSiteAltAllele = new VariantAlternateAllele(VcfReferenceBegin, VcfReferenceEnd,
VcfColumns[VcfCommon.RefIndex], ".");
// create alternative allele for reference no call
if (IsRefNoCall)
{
// the following are for refNoCall only.
refSiteAltAllele.NirvanaVariantType = VariantType.reference_no_call;
refSiteAltAllele.VepVariantType = VariantType.reference_no_call;
refSiteAltAllele.VariantId = _vid.Create(_renamer, ReferenceName, refSiteAltAllele);
}
AlternateAlleles.Add(refSiteAltAllele);
if (_fixGatkGenomeVcf)
{
RecoverGatkNonRefAllele();
}
return;
}
// split our alternate alleles
var altAlleles = VcfColumns[VcfCommon.AltIndex].Split(',');
var genotypeIndex = 1;
foreach (var altAllele in altAlleles)
{
AlternateAlleles.Add(new VariantAlternateAllele(VcfReferenceBegin, VcfReferenceEnd, VcfRefAllele, altAllele, genotypeIndex));
genotypeIndex++;
}
if (IsStructuralVariant)
{
FixMantaSvs(VcfColumns[VcfCommon.InfoIndex]);
}
if (IsStructuralVariant)
{
var infoEnd = ExtractInfoEnd();
if (infoEnd != null)
{
VcfReferenceEnd = (int)infoEnd;
}
var sv = ParseSvFields();
int?copyNumber = null;
if (CopyNumber != null)
{
copyNumber = CopyNumber;
}
else
{
if (AlternateAlleles.Count == 1 && AlternateAlleles.First().CopyNumber != null)
{
int altCopyNumber;
if (int.TryParse(AlternateAlleles.First().CopyNumber, out altCopyNumber))
{
copyNumber = altCopyNumber;
}
}
}
EvaluateCopyNumberType(copyNumber);
OverlapReferenceBegin = sv.MinBegin;
OverlapReferenceEnd = sv.MaxEnd;
}
else
{
TrimAlternateAlleles();
AssignVariantTypes();
AssignVariantIds();
}
if (_fixGatkGenomeVcf)
{
RecoverGatkNonRefAllele();
}
}
/// <summary>
/// assigns a variant type to the structural variant alternate allele
/// </summary>
public void AssignVariantType(VariantAlternateAllele altAllele, IAlleleTrimmer alleleTrimmer)
{
// sanity check: ignore unknown SV variant types
if (_variantType == VariantType.unknown)
{
// the only thing we do for unknown SV types is to increment the begin if it has a symbolic allele
if (altAllele.IsSymbolicAllele)
{
altAllele.Start++;
}
return;
}
var oldAltAllele = altAllele.AlternateAllele;
var has1KgCnv = false;
// add the copy number if applicable
if (_variantType == VariantType.copy_number_variation)
{
has1KgCnv = altAllele.IsSymbolicAllele && _copyNumber == "?";
altAllele.CopyNumber = has1KgCnv
? ExtractCopyNumberFromAltAllele(oldAltAllele)
: _copyNumber;
}
altAllele.IsStructuralVariant = true;
altAllele.VepVariantType = _variantType;
altAllele.NirvanaVariantType = _variantType;
altAllele.AlternateAllele = has1KgCnv ? ExtractCnvSymbolicAllele(oldAltAllele) : _altAllele;
// handle breakends
if (_breakEnds?.Count > 0)
{
altAllele.BreakEnds = new List <BreakEnd>();
altAllele.BreakEnds.AddRange(_breakEnds);
}
// update the reference begin position
//
// NOTE: If any of the ALT alleles is a symbolic allele (an angle-bracketed
// ID String “<ID>”) then the padding base is required and POS denotes
// the coordinate of the base preceding the polymorphism.
if (altAllele.IsSymbolicAllele)
{
altAllele.Start++;
}
else
{
// if the alt allele is not symbolic and its not a breakend, we call the regular trimmer
if (_variantType != VariantType.translocation_breakend)
{
altAllele.AlternateAllele = oldAltAllele;
alleleTrimmer.Trim(new List <VariantAlternateAllele> {
altAllele
});
}
}
// adjust the end coordinates after adjusted the begin
if (_svEnd != null)
{
altAllele.End = (int)_svEnd;
MaxEnd = Math.Max(MaxEnd, (int)_svEnd);
}
else if (_svLength != null)
{
altAllele.End = altAllele.Start + Math.Abs(_svLength.Value) - 1;
MaxEnd = Math.Max(MaxEnd, (int)_svLength);
}
// set the VID
altAllele.VariantId = _vid.Create(_renamer, _referenceName, altAllele);
}