private static ISupplementaryDataItem GetRefMinorItem(IList <ISupplementaryDataItem> saItems)
{
var totalAltAlleleFreq = 0.0;
var alleleFrequencies = new Dictionary <string, double>();
string refAllele = null;
foreach (var supplementaryDataItem in saItems)
{
var item = (AlleleFrequencyItem)supplementaryDataItem;
if (!IsSnv(item.RefAllele) || !IsSnv(item.AltAllele))
{
continue;
}
refAllele = item.RefAllele;
totalAltAlleleFreq += item.AltFrequency;
alleleFrequencies[item.AltAllele] = item.AltFrequency;
}
var isRefMinor = totalAltAlleleFreq >= SaCommon.RefMinorThreshold;
if (!isRefMinor)
{
return(null);
}
string globalMajor = SuppDataUtilities.GetMostFrequentAllele(alleleFrequencies, refAllele);
return(new RefMinorItem(saItems[0].Chromosome, saItems[0].Position, globalMajor));
}
