private void UpdateGeneSymbol(SpliceAiItem item)
{
if (_geneTree == null || _geneSynonyms == null)
{
return;
}
var chromosome = item.Chromosome;
var position = item.Position;
if (_currentPositionGeneSymbols.Count > 1)
{
return; //for multiple genes for a position, we cannot update the symbol
}
var nirvanaGenes = _geneTree.GetAllOverlappingValues(chromosome.Index, position, position);
if (nirvanaGenes == null)
{
item.Hgnc = null;
return;
}
var uniqueOverlapping = new HashSet <string>(nirvanaGenes);
if (uniqueOverlapping.Contains(item.Hgnc))
{
return;
}
//gene not found in cache
if (uniqueOverlapping.Count == 1)
{
item.Hgnc = uniqueOverlapping.First(); //update gene symbol
}
else
{
if (!_geneSynonyms.TryGetValue(item.Hgnc, out var symbolsList))
{
return;
}
var commonSymbols = symbolsList.Intersect(uniqueOverlapping).ToArray();
if (commonSymbols.Length == 1)
{
item.Hgnc = commonSymbols[0];
}
else
{
_unresolvedSymbols.Add(item.Hgnc);
}
}
}
public void GetAllOverlappingValues(ushort refIndex, int begin, int end, string[] expectedValues)
{
var observedValues = _intervalForest.GetAllOverlappingValues(refIndex, begin, end);
Assert.Equal(expectedValues, observedValues);
}