public void WritePosition(IEnumerable <SupplementaryDataItem> saItems)
{
if (saItems == null)
{
return;
}
var gnomadItems = new List <GnomadItem>();
foreach (var item in saItems)
{
if (!(item is GnomadItem gnomadItem))
{
throw new InvalidDataException("Expected GnomadItems list!!");
}
gnomadItems.Add(gnomadItem);
}
SupplementaryDataItem.RemoveConflictingAlleles(gnomadItems);
foreach (var gnomadItem in gnomadItems)
{
_writer.AddEntry(gnomadItem.Chromosome.EnsemblName, gnomadItem.Start, gnomadItem.ReferenceAllele, gnomadItem.AlternateAllele, null, new List <string> {
gnomadItem.GetJsonString()
});
}
}
public void WritePosition(IEnumerable <SupplementaryDataItem> saItems)
{
if (saItems == null)
{
return;
}
var onekGenItems = new List <OneKGenItem>();
foreach (var item in saItems)
{
if (!(item is OneKGenItem onekGenItem))
{
throw new InvalidDataException("Expected OnekGenItems list!!");
}
onekGenItems.Add(onekGenItem);
}
SupplementaryDataItem.RemoveConflictingAlleles(onekGenItems);
var totalAltAlleleFreq = 0.0;
var alleleFrequencies = new Dictionary <string, double>();
foreach (var onekGenItem in onekGenItems)
{
_onekgWriter.AddEntry(onekGenItem.Chromosome.EnsemblName, onekGenItem.Start,
onekGenItem.ReferenceAllele, onekGenItem.AlternateAllele,
onekGenItem.GetVcfString(), new List <string> {
onekGenItem.GetJsonString()
});
if (!IsSnv(onekGenItem.ReferenceAllele) || !IsSnv(onekGenItem.AlternateAllele))
{
continue;
}
if (onekGenItem.AllAlleleNumber != null && onekGenItem.AllAlleleCount != null)
{
var freq = 1.0 * onekGenItem.AllAlleleCount.Value / onekGenItem.AllAlleleNumber.Value;
totalAltAlleleFreq += freq;
alleleFrequencies[onekGenItem.AlternateAllele] = freq;
}
}
var isRefMinor = totalAltAlleleFreq >= SaDataBaseCommon.RefMinorThreshold;
if (isRefMinor)
{
_refMinorWriter.AddEntry(onekGenItems[0].Chromosome.EnsemblName, onekGenItems[0].Start, GetMajorAllele(alleleFrequencies), onekGenItems[0].ReferenceAllele);
}
}