//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 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;
}
}