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);
}
/// <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 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);
}
private void SetSaFields(SupplementaryPositionCreator saCreator, string newAltAllele)
{
var annotation = new ExacAnnotation
{
ExacCoverage = Coverage,
ExacAllAn = AllAlleleNumber,
ExacAfrAn = AfrAlleleNumber,
ExacAmrAn = AmrAlleleNumber,
ExacEasAn = EasAlleleNumber,
ExacFinAn = FinAlleleNumber,
ExacNfeAn = NfeAlleleNumber,
ExacOthAn = OthAlleleNumber,
ExacSasAn = SasAlleleNumber,
ExacAllAc = AllAlleleCount,
ExacAfrAc = AfrAlleleCount,
ExacAmrAc = AmrAlleleCount,
ExacEasAc = EasAlleleCount,
ExacFinAc = FinAlleleCount,
ExacNfeAc = NfeAlleleCount,
ExacOthAc = OthAlleleCount,
ExacSasAc = SasAlleleCount
};
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.Exac, newAltAllele, annotation);
}
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);
}
private void SetSaFields(SupplementaryPositionCreator saCreator, string newAltAllele)
{
var annotation = new EvsAnnotation
{
EvsAll = AllFreq,
EvsAfr = AfrFreq,
EvsEur = EurFreq,
EvsCoverage = Coverage,
NumEvsSamples = NumSamples
};
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.Evs, newAltAllele, annotation);
}
public void MergeSaCreator(SupplementaryPositionCreator other)
{
if (ReferencePosition != other.ReferencePosition || RefSeqName != other.RefSeqName)
{
return;
}
// first the allele specific annotations are merged
MergeAlleleSpecificAnnotations(other);
// merge positional annotations
MergePositionalAnnotations(other);
// merging custom annotations: they cannot be categorized into positional or otherwise since that is only known from each customItem's IsAlleleSpecificFlag
SaPosition.CustomItems.AddRange(other.SaPosition.CustomItems);
}
private void MergeAlleleSpecificAnnotations(SupplementaryPositionCreator other)
{
foreach (var otherAlleleAnnotation in other.SaPosition.AlleleSpecificAnnotations)
{
var otherAsa = otherAlleleAnnotation.Value;
AlleleSpecificAnnotation asa;
if (SaPosition.AlleleSpecificAnnotations.TryGetValue(otherAlleleAnnotation.Key, out asa))
{
asa.MergeAlleleSpecificAnnotation(otherAsa);
}
else
{
// this is for a new alternate allele
SaPosition.AlleleSpecificAnnotations[otherAlleleAnnotation.Key] = otherAsa;
}
}
}
private void MergePositionalAnnotations(SupplementaryPositionCreator other)
{
//TODO: figure out if this part is necessary, maybe we can calculate at the last step
if (!other.RefAlleleFreq.Equals(Double.MinValue))
{
RefAllele = other.RefAllele;
RefAlleleFreq = other.RefAlleleFreq;
}
// a cosmic id may have multiple entries each for a study. So this needs special handling
foreach (var cosmicItem in other.SaPosition.CosmicItems)
{
cosmicItem.AddCosmicToSa(this);
}
SaPosition.ClinVarItems.AddRange(other.SaPosition.ClinVarItems);
}
private void SetSaFields(SupplementaryPositionCreator saCreator, string newAltAllele)
{
if (!RefAlleleFreq.Equals(double.MinValue))
{
saCreator.RefAllele = ReferenceAllele;
saCreator.RefAlleleFreq = RefAlleleFreq;
}
//var sa = saCreator.SaPosition;
//set asa field
var annotation = new DbSnpAnnotation
{
DbSnp = new List <long> {
RsId
},
AltAlleleFreq = AltAlleleFreq
};
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.DbSnp, newAltAllele, annotation);
}
public void AddCosmicToSa(SupplementaryPositionCreator saCreator)
{
var sa = saCreator.SaPosition;
var index = sa.CosmicItems.IndexOf(this);
if (index == -1)
{
sa.CosmicItems.Add(this);
return;
}
//get the existing cosmic item in dictionary
if (sa.CosmicItems[index].Studies == null)
{
sa.CosmicItems[index].Studies = Studies;
return;
}
foreach (var study in Studies)
{
sa.CosmicItems[index].Studies.Add(study);
}
}
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);
}
private void SetSaFields(SupplementaryPositionCreator saCreator, string altAllele)
{
var annotation = new OneKGenAnnotation
{
AncestralAllele = AncestralAllele,
OneKgAllAn = AllAlleleNumber,
OneKgAfrAn = AfrAlleleNumber,
OneKgAmrAn = AmrAlleleNumber,
OneKgEurAn = EurAlleleNumber,
OneKgEasAn = EasAlleleNumber,
OneKgSasAn = SasAlleleNumber,
OneKgAllAc = AllAlleleCount,
OneKgAfrAc = AfrAlleleCount,
OneKgAmrAc = AmrAlleleCount,
OneKgEurAc = EurAlleleCount,
OneKgEasAc = EasAlleleCount,
OneKgSasAc = SasAlleleCount
};
saCreator.AddExternalDataToAsa(DataSourceCommon.DataSource.OneKg, altAllele, annotation);
}
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 abstract SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null);
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null)
{
return(null);
}
public override SupplementaryDataItem SetSupplementaryAnnotations(SupplementaryPositionCreator sa, string refBases = null)
{
throw new NotImplementedException();
}
