Exemplo n.º 1
0
        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);
                }
            }
        }
Exemplo n.º 2
0
        public void GetAllOverlappingValues(ushort refIndex, int begin, int end, string[] expectedValues)
        {
            var observedValues = _intervalForest.GetAllOverlappingValues(refIndex, begin, end);

            Assert.Equal(expectedValues, observedValues);
        }