/// <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 static void Read(ExtendedBinaryReader reader, SupplementaryAnnotationPosition sa)
{
sa.GlobalMinorAllele = reader.ReadAsciiString();
sa.GlobalMinorAlleleFrequency = reader.ReadAsciiString();
sa.GlobalMajorAllele = reader.ReadAsciiString();
sa.GlobalMajorAlleleFrequency = reader.ReadAsciiString();
// read the allele-specific records
var numAlleles = reader.ReadOptInt32();
for (var alleleIndex = 0; alleleIndex < numAlleles; alleleIndex++)
{
var allele = reader.ReadAsciiString();
var asa = AlleleSpecificAnnotation.Read(reader);
sa.AlleleSpecificAnnotations[allele] = asa;
}
// read cosmic records
var numCosmic = reader.ReadOptInt32();
for (var i = 0; i < numCosmic; i++)
{
var cosmicItem = new CosmicItem(reader);
sa.CosmicItems.Add(cosmicItem);
}
// read clinVar items
var numClinVar = reader.ReadOptInt32();
for (var i = 0; i < numClinVar; i++)
{
var clinVarItem = new ClinVarItem(reader);
sa.ClinVarItems.Add(clinVarItem);
}
// read custom annotation items
var numCustom = reader.ReadOptInt32();
for (var i = 0; i < numCustom; i++)
{
var customItem = new CustomItem(reader);
sa.CustomItems.Add(customItem);
}
}
