public void CreateFromTranslocation_InvalidAltAllele_ThrowException() { Assert.Throws <InvalidDataException>(delegate { var variant = new SimpleVariant(ChromosomeUtilities.Chr1, 100, 100, "A", "A{3:115024109{T", VariantType.translocation_breakend); // ReSharper disable once UnusedVariable BreakEndAdjacency[] adjacencies = BreakEndUtilities.CreateFromTranslocation(variant, ChromosomeUtilities.RefNameToChromosome); }); }
public void CreateFromTranslocation_Nominal(int position, string refAllele, string altAllele, bool expectedOnReverseStrand, string expectedPartnerChr, int expectedPartnerPosition, bool expectedPartnerOnReverseStrand) { var variant = new SimpleVariant(ChromosomeUtilities.Chr1, position, position, refAllele, altAllele, VariantType.translocation_breakend); BreakEndAdjacency[] adjacencies = BreakEndUtilities.CreateFromTranslocation(variant, ChromosomeUtilities.RefNameToChromosome); Assert.NotNull(adjacencies); Assert.Single(adjacencies); var observed = adjacencies[0]; Assert.Equal(expectedOnReverseStrand, observed.Origin.OnReverseStrand); Assert.Equal(expectedPartnerChr, observed.Partner.Chromosome.EnsemblName); Assert.Equal(expectedPartnerPosition, observed.Partner.Position); Assert.Equal(expectedPartnerOnReverseStrand, observed.Partner.OnReverseStrand); }
private static BreakEndAdjacency[] GetBreakEndAdjacencies(ISimpleVariant variant, IDictionary <string, IChromosome> refNameToChromosome) => variant.Type == VariantType.translocation_breakend ? BreakEndUtilities.CreateFromTranslocation(variant, refNameToChromosome) : BreakEndUtilities.CreateFromSymbolicAllele(variant, variant.Type);