private void WritePosition(List <ISupplementaryDataItem> items)
{
int position = items[0].Position;
_memStream.Position = 0;
if (_isPositional)
{
var positionalItem = SuppDataUtilities.GetPositionalAnnotation(items);
if (positionalItem == null)
{
return;
}
_memWriter.Write(positionalItem.GetJsonString());
}
else
{
// any data source that is reported by allele and is not an array (e.g. allele frequencies) need this filtering step
if (_index.MatchByAllele && !_index.IsArray)
{
items = SuppDataUtilities.RemoveConflictingAlleles(items, _throwErrorOnConflicts);
}
if (_index.JsonKey == SaCommon.PrimateAiTag)
{
items = SuppDataUtilities.DeDuplicatePrimateAiItems(items);
}
_memWriter.WriteOpt(items.Count);
foreach (ISupplementaryDataItem saItem in items)
{
_memWriter.WriteOptAscii(saItem.RefAllele);
_memWriter.WriteOptAscii(saItem.AltAllele);
_memWriter.Write(saItem.GetJsonString());
}
}
int numBytes = (int)_memStream.Position;
if (!_block.HasSpace(numBytes))
{
Flush(items[0].Chromosome.Index);
}
_block.Add(_memBuffer, numBytes, position);
}
public void ResolveDuplicates()
{
var entrezToHgnc = new Dictionary <string, string>
{
{ "255403", "Gene1" }
};
var ensemblToHgnc = new Dictionary <string, string>
{
{ "ENSG00000234810", "Gene2" }
};
var primateParser = new PrimateAiParser(GetDuplicateItemStream(), GetSequenceProvider(), entrezToHgnc, ensemblToHgnc);
var items = primateParser.GetItems().Cast <ISupplementaryDataItem>().ToList();
var deDupItems = SuppDataUtilities.DeDuplicatePrimateAiItems(items);
Assert.Single(deDupItems);
Assert.Equal("\"hgnc\":\"Gene1\",\"scorePercentile\":0.93", deDupItems[0].GetJsonString());
}
