public void MergeAlleleSpecificAnnotation(AlleleSpecificAnnotation otherAsa)
{
foreach (var dataSource in DataSourceCommon.GetAllDataSources())
{
var index = DataSourceCommon.GetIndex(dataSource);
if (HasDataSource(dataSource) && otherAsa.HasDataSource(dataSource))
{
Annotations[index].MergeAnnotations(otherAsa.Annotations[index]);
break;
}
if (!HasDataSource(dataSource) && otherAsa.HasDataSource(dataSource))
{
DataSourceCommon.AddDataSource(dataSource, ref SaDataSourceFlag);
Annotations[index] = otherAsa.Annotations[index];
}
}
}
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);
}
}
public static AlleleSpecificAnnotation Read(ExtendedBinaryReader reader)
{
var asa = new AlleleSpecificAnnotation {
SaDataSourceFlag = reader.ReadByte()
};
foreach (var dataSource in DataSourceCommon.GetAllDataSources())
{
if (!asa.HasDataSource(dataSource))
{
continue;
}
var supplementaryAnnotation = SupplementaryAnnotationFactory.CreateSupplementaryAnnotation(dataSource);
supplementaryAnnotation.Read(reader);
asa.Annotations[DataSourceCommon.GetIndex(dataSource)] = supplementaryAnnotation;
}
return(asa);
}
