public void MergeAnnotations(ISupplementaryAnnotation other)
{
var otherAnnotation = other as OneKGenAnnotation;
if (otherAnnotation?.OneKgAllAn == null)
{
return;
}
if (OneKgAllAc == null)
{
AncestralAllele = otherAnnotation.AncestralAllele;
OneKgAllAn = otherAnnotation.OneKgAllAn;
OneKgAfrAn = otherAnnotation.OneKgAfrAn;
OneKgAmrAn = otherAnnotation.OneKgAmrAn;
OneKgEurAn = otherAnnotation.OneKgEurAn;
OneKgEasAn = otherAnnotation.OneKgEasAn;
OneKgSasAn = otherAnnotation.OneKgSasAn;
OneKgAllAc = otherAnnotation.OneKgAllAc;
OneKgAfrAc = otherAnnotation.OneKgAfrAc;
OneKgAmrAc = otherAnnotation.OneKgAmrAc;
OneKgEurAc = otherAnnotation.OneKgEurAc;
OneKgEasAc = otherAnnotation.OneKgEasAc;
OneKgSasAc = otherAnnotation.OneKgSasAc;
}
else
{
HasConflicts = true;
Clear();
}
}
public void MergeAnnotations(ISupplementaryAnnotation other)
{
var otherAnnotation = other as DbSnpAnnotation;
if (otherAnnotation?.DbSnp == null || otherAnnotation.DbSnp.Count == 0)
{
return;
}
DbSnp.AddRange(otherAnnotation.DbSnp.Where(x => !DbSnp.Contains(x)));
if (otherAnnotation.AltAlleleFreq > double.MinValue)
{
AltAlleleFreq = otherAnnotation.AltAlleleFreq;
}
}
public void MergeAnnotations(ISupplementaryAnnotation other)
{
var otherAnnotation = other as ExacAnnotation;
if (otherAnnotation?.ExacAllAn == null || otherAnnotation.ExacAllAn.Value == 0 || HasConflicts)
{
return;
}
if (ExacAllAn == null || ExacAllAn.Value == 0)
{
ExacCoverage = otherAnnotation.ExacCoverage;
ExacAllAn = otherAnnotation.ExacAllAn;
ExacAfrAn = otherAnnotation.ExacAfrAn;
ExacAmrAn = otherAnnotation.ExacAmrAn;
ExacEasAn = otherAnnotation.ExacEasAn;
ExacFinAn = otherAnnotation.ExacFinAn;
ExacNfeAn = otherAnnotation.ExacNfeAn;
ExacOthAn = otherAnnotation.ExacOthAn;
ExacSasAn = otherAnnotation.ExacSasAn;
ExacAllAc = otherAnnotation.ExacAllAc;
ExacAfrAc = otherAnnotation.ExacAfrAc;
ExacAmrAc = otherAnnotation.ExacAmrAc;
ExacEasAc = otherAnnotation.ExacEasAc;
ExacFinAc = otherAnnotation.ExacFinAc;
ExacNfeAc = otherAnnotation.ExacNfeAc;
ExacOthAc = otherAnnotation.ExacOthAc;
ExacSasAc = otherAnnotation.ExacSasAc;
}
else
{
// this is a conflict
HasConflicts = true;
Clear();
}
}
public void MergeAnnotations(ISupplementaryAnnotation other)
{
var otherAnnotation = other as EvsAnnotation;
if (otherAnnotation?.NumEvsSamples == null)
{
return;
}
if (NumEvsSamples == null)
{
EvsAll = otherAnnotation.EvsAll;
EvsAfr = otherAnnotation.EvsAfr;
EvsEur = otherAnnotation.EvsEur;
EvsCoverage = otherAnnotation.EvsCoverage;
NumEvsSamples = otherAnnotation.NumEvsSamples;
}
else
{
HasConflicts = true;
Clear();
}
}
public void AddExternalDataToAsa(DataSourceCommon.DataSource dataSource, string altAllele, ISupplementaryAnnotation annotation)
{
if (annotation == null)
{
return;
}
var dataSourceIndex = DataSourceCommon.GetIndex(dataSource);
if (!SaPosition.AlleleSpecificAnnotations.ContainsKey(altAllele))
{
SaPosition.AlleleSpecificAnnotations[altAllele] = new AlleleSpecificAnnotation();
DataSourceCommon.AddDataSource(dataSource, ref SaPosition.AlleleSpecificAnnotations[altAllele].SaDataSourceFlag);
SaPosition.AlleleSpecificAnnotations[altAllele].Annotations[dataSourceIndex] =
annotation;
return;
}
if (!SaPosition.AlleleSpecificAnnotations[altAllele].HasDataSource(dataSource))
{
DataSourceCommon.AddDataSource(dataSource, ref SaPosition.AlleleSpecificAnnotations[altAllele].SaDataSourceFlag);
SaPosition.AlleleSpecificAnnotations[altAllele].Annotations[dataSourceIndex] =
annotation;
return;
}
SaPosition.AlleleSpecificAnnotations[altAllele].Annotations[dataSourceIndex].MergeAnnotations(annotation);
}
