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()
});
}
}
private void AddAdditionalItems(SupplementaryDataItem minSupplementaryDataItem, SupplementaryPositionCreator sa)
{
if (_additionalItemsList.Count <= 0)
{
return;
}
if (_additionalItemsList.Count > 1)
{
_additionalItemsList.Sort();
}
while (_additionalItemsList.Count > 0)
{
var firstItem = _additionalItemsList[0];
if (firstItem.Equals(minSupplementaryDataItem))
{
firstItem.SetSupplementaryAnnotations(sa);
_additionalItemsList.RemoveAt(0);
}
else
{
break;
}
}
}
private SupplementaryDataItem CurrentMinSupplementaryDataItem()
{
SupplementaryDataItem minSupplementaryDataItem = null;
foreach (var iDataEnumerator in _iSupplementaryDataItemList)
{
if (minSupplementaryDataItem == null)
{
minSupplementaryDataItem = iDataEnumerator.Current;
}
else
if (minSupplementaryDataItem.CompareTo(iDataEnumerator.Current) > 0)
{
minSupplementaryDataItem = iDataEnumerator.Current;
}
}
// checking if one of the additional items is the min.
if (_additionalItemsList.Count <= 0)
{
return(minSupplementaryDataItem);
}
if (minSupplementaryDataItem == null)
{
return(_additionalItemsList[0]);
}
if (minSupplementaryDataItem.CompareTo(_additionalItemsList[0]) > 0)
{
minSupplementaryDataItem = _additionalItemsList[0];
}
return(minSupplementaryDataItem);
}
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);
}
}
