public IEnumerable <ISupplementaryDataItem> GetItems()
{
var vcvList = GetVariationRecords();
Console.WriteLine($"Found {vcvList.Count} VCV records");
var unknownVcvs = new HashSet <int>();
foreach (var clinVarItem in GetRcvItems())
{
if (clinVarItem.VariationId == null)
{
yield return(clinVarItem);
continue;
}
var vcvId = clinVarItem.VariationId.Value;
var vcvIndex = SuppDataUtilities.BinarySearch(vcvList, vcvId);
if (vcvIndex < 0)
{
Console.WriteLine($"Unknown vcv id:{vcvId} found in {clinVarItem.Id}");
unknownVcvs.Add(vcvId);
//remove the VariationId
yield return(new ClinVarItem(clinVarItem.Chromosome, clinVarItem.Position, clinVarItem.Stop,
clinVarItem.RefAllele, clinVarItem.AltAllele, clinVarItem.JsonSchema, clinVarItem.AlleleOrigins,
clinVarItem.VariantType, clinVarItem.Id, null, clinVarItem.ReviewStatus,
clinVarItem.MedGenIds, clinVarItem.OmimIds, clinVarItem.OrphanetIds,
clinVarItem.Phenotypes, clinVarItem.Significances, clinVarItem.PubmedIds, clinVarItem.LastUpdatedDate));
continue;
}
var vcvItem = vcvList[vcvIndex];
yield return(new VcvSaItem(clinVarItem.Chromosome, clinVarItem.Position, clinVarItem.RefAllele, clinVarItem.AltAllele,
vcvItem.Accession, vcvItem.Version, vcvItem.LastUpdatedDate, vcvItem.ReviewStatus, vcvItem.Significances));
yield return(clinVarItem);
}
Console.WriteLine($"{unknownVcvs.Count} unknown VCVs found in RCVs.");
Console.WriteLine($"{string.Join(',', unknownVcvs)}");
}
public IEnumerable <ISupplementaryDataItem> GetItems()
{
_vcvItems = GetVariationRecords();
Console.WriteLine($"Found {_vcvItems.Count} VCV records");
var unknownVcvs = new HashSet <int>();
foreach (var clinVarItem in GetRcvItems())
{
if (string.IsNullOrEmpty(clinVarItem.VariationId))
{
yield return(clinVarItem);
continue;
}
var vcvId = int.Parse(clinVarItem.VariationId);
var vcvIndex = SuppDataUtilities.BinarySearch(_vcvItems, vcvId);
if (vcvIndex < 0)
{
Console.WriteLine($"Unknown vcv id:{vcvId} found in {clinVarItem.Id}");
unknownVcvs.Add(vcvId);
//remove the VariationId
clinVarItem.VariationId = null;
yield return(clinVarItem);
continue;
}
var vcvItem = _vcvItems[vcvIndex];
yield return(new VcvSaItem(clinVarItem.Chromosome, clinVarItem.Position, clinVarItem.RefAllele, clinVarItem.AltAllele,
vcvItem.Accession, vcvItem.Version, vcvItem.LastUpdatedDate, vcvItem.ReviewStatus, vcvItem.Significances));
clinVarItem.VariationId = $"{vcvItem.Accession}.{vcvItem.Version}";
yield return(clinVarItem);
}
Console.WriteLine($"{unknownVcvs.Count} unknown VCVs found in RCVs.");
Console.WriteLine($"{string.Join(',', unknownVcvs)}");
}
