public void Clear()
{
SupplementaryAnnotationPosition = null;
ReferenceName = null;
UcscReferenceName = null;
EnsemblReferenceName = null;
VcfRefAllele = null;
VcfColumns = null;
ConservationScore = null;
CytogeneticBand = null;
VcfVariantId = null;
IsRefMinor = false;
IsSingletonRefSite = false;
IsReference = false;
IsRefNoCall = false;
IsStructuralVariant = false;
VcfReferenceBegin = 0;
VcfReferenceEnd = 0;
OverlapReferenceBegin = 0;
OverlapReferenceEnd = 0;
StrandBias = null;
JointSomaticNormalQuality = null;
RecalibratedQuality = null;
CiPos = null;
CiEnd = null;
CopyNumber = null;
Depth = null;
InternalCopyNumberType = VariantType.unknown;
SvLength = null;
ColocalizedWithCnv = false;
AlternateAlleles?.Clear();
_overlappingSupplementaryIntervals?.Clear();
}
public void AddCustomAnnotation(ISupplementaryAnnotationPosition sa)
{
// sanity check: SVs don't use supplementary annotations for now
if (IsStructuralVariant)
{
return;
}
sa.SetIsAlleleSpecific(SuppAltAllele);
if (SupplementaryAnnotationPosition == null)
{
SupplementaryAnnotationPosition = sa;
return;
}
if (SupplementaryAnnotationPosition.CustomItems != null)
{
SupplementaryAnnotationPosition.CustomItems.AddRange(sa.CustomItems);
}
else
{
SupplementaryAnnotationPosition.CustomItems = sa.CustomItems;
}
}
/// <summary>
/// sets the supplementary annotation allele
/// </summary>
public void SetSupplementaryAnnotation(ISupplementaryAnnotationPosition sa)
{
// sanity check: SVs don't use supplementary annotations for now
if (IsStructuralVariant)
{
return;
}
sa.SetIsAlleleSpecific(SuppAltAllele);
SupplementaryAnnotationPosition = sa;
}
/// <summary>
/// sets the supplementary annotation record for each allele in this record
/// </summary>
public void SetSupplementaryAnnotation(ISupplementaryAnnotationReader saReader)
{
// for ref variants, alternate alleles will be empty. We will need to pull the SA from reference position.
// If this is a ref minor position, I will add an alt allele with the ref as alt and GMAF as ref
if (IsReference)
{
// checking the index for refMinor using the index before actually going to disk
IsRefMinor = saReader.IsRefMinor(VcfReferenceBegin);
if (!IsRefMinor)
{
return;
}
SupplementaryAnnotationPosition = saReader.GetAnnotation(VcfReferenceBegin);
if (SupplementaryAnnotationPosition == null)
{
return;
}
// if we have a ref minor, we do not care about ref no call
IsRefNoCall = false;
AlternateAlleles[0].AlternateAllele = AlternateAlleles[0].ReferenceAllele;// ref becomes alt for ref minor
if (SupplementaryAnnotationPosition.GlobalMajorAllele != null)
{
AlternateAlleles[0].ReferenceAllele = SupplementaryAnnotationPosition.GlobalMajorAllele;
}
AlternateAlleles[0].NirvanaVariantType = VariantType.SNV;
AlternateAlleles[0].VepVariantType = VariantType.SNV;
AlternateAlleles[0].SuppAltAllele = AlternateAlleles[0].AlternateAllele; // for SNVs there is nothing to reduce
AlternateAlleles[0].VariantId = _vid.Create(_renamer, EnsemblReferenceName, AlternateAlleles[0]);
AlternateAlleles[0].SetSupplementaryAnnotation(SupplementaryAnnotationPosition);
return;
}
foreach (var altAllele in AlternateAlleles)
{
var sa = saReader.GetAnnotation(altAllele.Start);
if (sa != null)
{
altAllele.SetSupplementaryAnnotation(sa);
}
}
}
/// <summary>
/// copy constructor
/// </summary>
public VariantAlternateAllele(VariantAlternateAllele altAllele)
{
AlternateAllele = altAllele.AlternateAllele;
BreakEnds = altAllele.BreakEnds;
ConservationScore = altAllele.ConservationScore;
CopyNumber = altAllele.CopyNumber;
GenotypeIndex = altAllele.GenotypeIndex;
_isForwardTranscriptDuplicate = altAllele._isForwardTranscriptDuplicate;
_isReverseTranscriptDuplicate = altAllele._isReverseTranscriptDuplicate;
IsStructuralVariant = altAllele.IsStructuralVariant;
IsSymbolicAllele = altAllele.IsSymbolicAllele;
NirvanaVariantType = altAllele.NirvanaVariantType;
ReferenceAllele = altAllele.ReferenceAllele;
Start = altAllele.Start;
End = altAllele.End;
SuppAltAllele = altAllele.SuppAltAllele;
SupplementaryAnnotationPosition = altAllele.SupplementaryAnnotationPosition;
VariantId = altAllele.VariantId;
VepVariantType = altAllele.VepVariantType;
}
public void AddCustomAnnotation(List <ISupplementaryAnnotationReader> saReaders)
{
if (IsReference)
{
foreach (var saReader in saReaders)
{
var sa = saReader.GetAnnotation(VcfReferenceBegin);
if (sa == null)
{
continue;
}
if (SupplementaryAnnotationPosition != null)
{
SupplementaryAnnotationPosition.CustomItems.AddRange(sa.CustomItems);
}
else
{
SupplementaryAnnotationPosition = sa;
}
}
return;
}
foreach (var altAllele in AlternateAlleles)
{
foreach (var saReader in saReaders)
{
var sa = saReader.GetAnnotation(altAllele.Start);
if (sa != null)
{
altAllele.AddCustomAnnotation(sa);
}
}
}
}
/// <summary>
/// constructor
/// </summary>
public MockSupplementaryAnnotationReader(SupplementaryAnnotationPosition saPosition)
{
_saPosition = saPosition;
_referencePosition = saPosition.ReferencePosition;
_isRefMinorAllele = saPosition.IsRefMinorAllele;
}
