//constructors
public CosmicItem(ExtendedBinaryReader reader)
{
if (reader == null)
{
return;
}
ID = reader.ReadAsciiString();
SaAltAllele = reader.ReadAsciiString();
AltAllele = SupplementaryAnnotationUtilities.ReverseSaReducedAllele(SaAltAllele);
RefAllele = reader.ReadAsciiString();
Gene = reader.ReadAsciiString();
SampleCount = reader.ReadOptNullableInt32();
var countStudy = reader.ReadOptInt32();
if (countStudy > 0)
{
Studies = new HashSet <CosmicStudy>();
}
for (var i = 0; i < countStudy; i++)
{
Studies.Add(new CosmicStudy(reader));
}
}
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);
}
/// <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.
}
// 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 void Write(ExtendedBinaryWriter writer)
{
writer.WriteOptArray(_alleleOrigins?.Distinct().ToArray(), writer.WriteOptAscii);
writer.WriteOptAscii(SaAltAllele);
writer.WriteOptAscii(ReferenceAllele);
writer.WriteOptAscii(ID);
writer.Write((byte)ReviewStatus);
writer.WriteOptAscii(IsAlleleSpecific);
writer.WriteOptArray(_medgenIds?.Distinct().ToArray(), writer.WriteOptAscii);
writer.WriteOptArray(_omimIds?.Distinct().ToArray(), writer.WriteOptAscii);
writer.WriteOptArray(_orphanetIds?.Distinct().ToArray(), writer.WriteOptAscii);
writer.WriteOptArray(SupplementaryAnnotationUtilities.ConvertMixedFormatStrings(_phenotypes)?.Distinct().ToArray(), writer.WriteOptUtf8);
writer.WriteOptAscii(Significance);
writer.WriteOpt(LastUpdatedDate);
writer.WriteOptArray(_pubmedIds.ToArray(), writer.WriteOpt);
}
public ClinVarItem(ExtendedBinaryReader reader)
{
_alleleOrigins = reader.ReadOptArray(reader.ReadAsciiString)?.ToList();
SaAltAllele = reader.ReadAsciiString();
AltAllele = SaAltAllele != null?SupplementaryAnnotationUtilities.ReverseSaReducedAllele(SaAltAllele) : ""; // A
ReferenceAllele = reader.ReadAsciiString();
ID = reader.ReadAsciiString();
ReviewStatus = (ReviewStatusEnum)reader.ReadByte();
IsAlleleSpecific = reader.ReadAsciiString();
_medgenIds = reader.ReadOptArray(reader.ReadAsciiString)?.ToList();
_omimIds = reader.ReadOptArray(reader.ReadAsciiString)?.ToList();
_orphanetIds = reader.ReadOptArray(reader.ReadAsciiString)?.ToList();
_phenotypes = reader.ReadOptArray(reader.ReadUtf8String)?.ToList();
Significance = reader.ReadAsciiString();
LastUpdatedDate = reader.ReadOptInt64();
_pubmedIds = reader.ReadOptArray(reader.ReadOptInt64)?.ToList();
}
public CustomItem(ExtendedBinaryReader reader)
{
Id = reader.ReadAsciiString();
AnnotationType = reader.ReadAsciiString();
SaAltAllele = reader.ReadAsciiString();
AltAllele = SupplementaryAnnotationUtilities.ReverseSaReducedAllele(SaAltAllele);
IsPositional = reader.ReadBoolean();
var numStringFields = reader.ReadOptInt32();
if (numStringFields > 0)
{
StringFields = new Dictionary <string, string>();
for (var i = 0; i < numStringFields; i++)
{
var key = reader.ReadAsciiString();
var value = reader.ReadAsciiString();
StringFields[key] = value;
}
}
else
{
StringFields = null;
}
var numBoolFields = reader.ReadOptInt32();
if (numBoolFields > 0)
{
BooleanFields = new List <string>();
for (var i = 0; i < numBoolFields; i++)
{
BooleanFields.Add(reader.ReadAsciiString());
}
}
else
{
BooleanFields = 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);
}
