/// <summary>
/// Adds the ClinVar items in this object to the supplementary annotation object
/// </summary>
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator saCreator, string refBases = null)
{
// check if the ref allele matches the refBases as a prefix
if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases))
{
return(null); //the ref allele for this entry did not match the reference bases.
}
// for insertions and deletions, the alternate allele has to be modified to conform with VEP convension
var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AltAllele);
var newStart = newAlleles.Item1;
var newRefAllele = newAlleles.Item2;
var newAltAllele = newAlleles.Item3;
if (newRefAllele != ReferenceAllele)
{
var additionalItem = new ClinVarItem(Chromosome, newStart, _alleleOrigins, newAltAllele, ID, ReviewStatusString, _medgenIds, _omimIds, _orphanetIds, _phenotypes, newRefAllele, Significance, _pubmedIds, LastUpdatedDate);
return(additionalItem);
}
saCreator.SaPosition.ClinVarItems.Add(new ClinVarItem(Chromosome, newStart, _alleleOrigins, newAltAllele, ID, ReviewStatusString, _medgenIds, _omimIds, _orphanetIds, _phenotypes, newRefAllele, Significance, _pubmedIds, LastUpdatedDate));
return(null);
}
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null)
{
// check if the ref allele matches the refBases as a prefix
if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases))
{
return(null); //the ref allele for this entry did not match the reference bases.
}
var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AlternateAllele);
var newStart = newAlleles.Item1;
var newRefAllele = newAlleles.Item2;
var newAltAllele = newAlleles.Item3;
if (newRefAllele != ReferenceAllele)
{
return(new DbSnpItem(Chromosome,
newStart,
RsId,
newRefAllele,
RefAlleleFreq,
newAltAllele,
AltAlleleFreq,
_infoField)); // we need to keep the vcfline for the sake of conflict resolution
}
// it's a SNV or MNV at this position
SetSaFields(sa, newAltAllele);
return(null);
}
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null)
{
// check if the ref allele matches the refBases as a prefix
if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases))
{
return(null); //the ref allele for this entry did not match the reference bases.
}
// if this is a SV,
if (IsInterval)
{
return(null);
}
var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AlternateAllele);
var newStart = newAlleles.Item1;
var newRefAllele = newAlleles.Item2;
var newAltAllele = newAlleles.Item3;
if (newRefAllele != ReferenceAllele)
{
return(new OneKGenItem(Chromosome, newStart, Id, newRefAllele, newAltAllele, AncestralAllele,
AllAlleleCount, AfrAlleleCount, AmrAlleleCount, EurAlleleCount, EasAlleleCount, SasAlleleCount,
AllAlleleNumber, AfrAlleleNumber, AmrAlleleNumber, EurAlleleNumber, EasAlleleNumber, SasAlleleNumber,
SvType, SvEnd, CiPos, CiEnd));
}
SetSaFields(sa, newAltAllele);
return(null);
}
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator saCreator, string refBases = null)
{
// check if the ref allele matches the refBases as a prefix
if (!SupplementaryAnnotationUtilities.ValidateRefAllele(RefAllele, refBases))
{
return(null); //the ref allele for this entry did not match the reference bases.
}
var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, RefAllele, AltAllele);
var newStart = newAlleles.Item1;
var newRefAllele = newAlleles.Item2;
var newAltAllele = newAlleles.Item3;
if (newRefAllele != RefAllele)
{
return(new CosmicItem(Chromosome, newStart, ID, newRefAllele, newAltAllele, Gene, Studies, SampleCount));
}
var newRefAlleleParsed = string.IsNullOrEmpty(newRefAllele) ? "-" : newRefAllele;
var newItem = new CosmicItem(Chromosome, Start, ID, newRefAlleleParsed, newAltAllele, Gene, Studies, SampleCount);
newItem.AddCosmicToSa(saCreator);
return(null);
}
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null)
{
// check if the ref allele matches the refBases as a prefix
if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases))
{
return(null); //the ref allele for this entry did not match the reference bases.
}
var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AlternateAllele);
var newStart = newAlleles.Item1;
var newRefAllele = newAlleles.Item2;
var newAltAllele = newAlleles.Item3;
if (newRefAllele != ReferenceAllele)
{
return(new ExacItem(Chromosome, newStart, newRefAllele, newAltAllele, Coverage,
AllAlleleNumber, AfrAlleleNumber, AmrAlleleNumber, EasAlleleNumber, FinAlleleNumber, NfeAlleleNumber, OthAlleleNumber, SasAlleleNumber,
AllAlleleCount, AfrAlleleCount, AmrAlleleCount, EasAlleleCount, FinAlleleCount, NfeAlleleCount, OthAlleleCount, SasAlleleCount));
}
SetSaFields(sa, newAltAllele);
return(null);
}
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator saCreator, string refBases = null)
{
// check if the ref allele matches the refBases as a prefix
if (!SupplementaryAnnotationUtilities.ValidateRefAllele(RefAllele, refBases))
{
return(null); //the ref allele for this entry did not match the reference bases.
}
var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, RefAllele, AltAllele);
var newStart = newAlleles.Item1;
var newRefAllele = newAlleles.Item2;
var newAltAllele = newAlleles.Item3;
if (newRefAllele != RefAllele)
{
return(new CustomItem(Chromosome, newStart, newRefAllele, newAltAllele, AnnotationType, Id, IsPositional, StringFields, BooleanFields));
}
//for ins, del, indel without padding base, the altAllele will change even though the ref does not.
saCreator.SaPosition.CustomItems.Add(new CustomItem(Chromosome, newStart, newRefAllele, newAltAllele, AnnotationType, Id, IsPositional, StringFields, BooleanFields));
return(null);
}
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null)
{
// check if the ref allele matches the refBases as a prefix
if (!SupplementaryAnnotationUtilities.ValidateRefAllele(ReferenceAllele, refBases))
{
return(null); //the ref allele for this entry did not match the reference bases.
}
var newAlleles = SupplementaryAnnotationUtilities.GetReducedAlleles(Start, ReferenceAllele, AlternateAllele);
var newStart = newAlleles.Item1;
var newRefAllele = newAlleles.Item2;
var newAltAllele = newAlleles.Item3;
if (newRefAllele != ReferenceAllele)
{
return(new EvsItem(Chromosome, newStart, RsId, newRefAllele, newAltAllele, AllFreq, AfrFreq, EurFreq, Coverage, NumSamples));
}
SetSaFields(sa, newAltAllele);
return(null);
}