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);
}
}
