public void ClinVarUnknownAllele() { var annotatedVariant = DataUtilities.GetVariant(DataUtilities.EmptyCachePrefix, Resources.MiniSuppAnnot("chr13_40298637_40298638.nsa"), "chr1 40298637 . TTA T 222 PASS CIGAR=1M2D"); Assert.NotNull(annotatedVariant); var altAllele = annotatedVariant.AnnotatedAlternateAlleles.First(); Assert.NotNull(altAllele); Assert.Equal("chr1", altAllele.ReferenceName); Assert.Equal(40298638, altAllele.ReferenceBegin); Assert.Equal("deletion", altAllele.VariantType); Assert.Equal("1:40298638:40298639", altAllele.VariantId); AssertUtilities.CheckAlleleCoverage(altAllele, 45, "ExacCoverage"); AssertUtilities.CheckAlleleFrequencies(altAllele, 0.073456, "ExacAlleleFrequencyAll"); AssertUtilities.CheckAlleleFrequencies(altAllele, 0.046417, "ExacAlleleFrequencyAfrican"); AssertUtilities.CheckAlleleFrequencies(altAllele, 0.169241, "ExacAlleleFrequencyAmerican"); AssertUtilities.CheckAlleleFrequencies(altAllele, 0.078326, "ExacAlleleFrequencyEastAsian"); AssertUtilities.CheckAlleleFrequencies(altAllele, 0.05431, "ExacAlleleFrequencyFinish"); AssertUtilities.CheckAlleleFrequencies(altAllele, 0.056521, "ExacAlleleFrequencyNonFinish"); AssertUtilities.CheckAlleleFrequencies(altAllele, 0.088235, "ExacAlleleFrequencyOther"); AssertUtilities.CheckAlleleFrequencies(altAllele, 0.109281, "ExacAlleleFrequencySouthAsian"); // ReSharper disable once PossibleNullReferenceException foreach (var clinVarEntry in altAllele.ClinVarEntries) { Assert.Equal("RCV000082046.4", clinVarEntry.ID); Assert.Equal("germline", clinVarEntry.AlleleOrigins.First()); Assert.Equal("not_specified", clinVarEntry.Phenotypes.First()); Assert.Equal("CN169374", clinVarEntry.MedGenIDs.First()); Assert.Equal("Benign", clinVarEntry.Significance); } var cosmicEntry = altAllele.CosmicEntries.ElementAt(1); Assert.NotNull(cosmicEntry); Assert.Equal("COSM3730300", cosmicEntry.ID); Assert.Equal("true", cosmicEntry.IsAlleleSpecific); Assert.Equal("-", cosmicEntry.AltAllele); Assert.Equal("COG6", cosmicEntry.Gene); // ReSharper disable once PossibleNullReferenceException foreach (var cosmicStudy in cosmicEntry.Studies) { Assert.Equal("carcinoma", cosmicStudy.Histology); Assert.Equal("oesophagus", cosmicStudy.PrimarySite); } cosmicEntry = altAllele.CosmicEntries.ElementAt(2); Assert.NotNull(cosmicEntry); Assert.Equal("COSM3730301", cosmicEntry.ID); Assert.Equal("true", cosmicEntry.IsAlleleSpecific); Assert.Equal("-", cosmicEntry.AltAllele); Assert.Equal("COG6_ENST00000416691", cosmicEntry.Gene); // ReSharper disable once PossibleNullReferenceException foreach (var cosmicStudy in cosmicEntry.Studies) { Assert.Equal("carcinoma", cosmicStudy.Histology); Assert.Equal("oesophagus", cosmicStudy.PrimarySite); } }