public void CreateFromSymbolicAllele_Duplication() { var interval = new ChromosomeInterval(ChromosomeUtilities.Chr1, 37820921, 38404543); BreakEndAdjacency[] adjacencies = BreakEndUtilities.CreateFromSymbolicAllele(interval, VariantType.tandem_duplication); Assert.NotNull(adjacencies); Assert.Equal(2, adjacencies.Length); var observed = adjacencies[0]; Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed.Origin.Chromosome.EnsemblName); Assert.Equal(38404543, observed.Origin.Position); Assert.False(observed.Origin.OnReverseStrand); Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed.Partner.Chromosome.EnsemblName); Assert.Equal(37820920, observed.Partner.Position); Assert.False(observed.Partner.OnReverseStrand); var observed2 = adjacencies[1]; Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed2.Origin.Chromosome.EnsemblName); Assert.Equal(37820920, observed2.Origin.Position); Assert.True(observed2.Origin.OnReverseStrand); Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed2.Partner.Chromosome.EnsemblName); Assert.Equal(38404543, observed2.Partner.Position); Assert.True(observed2.Partner.OnReverseStrand); }
public void CreateFromSymbolicAllele_Deletion() { var interval = new ChromosomeInterval(ChromosomeUtilities.Chr1, 1594584, 1660503); BreakEndAdjacency[] adjacencies = BreakEndUtilities.CreateFromSymbolicAllele(interval, VariantType.deletion); Assert.NotNull(adjacencies); Assert.Equal(2, adjacencies.Length); var observed = adjacencies[0]; Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed.Origin.Chromosome.EnsemblName); Assert.Equal(1594583, observed.Origin.Position); Assert.False(observed.Origin.OnReverseStrand); Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed.Partner.Chromosome.EnsemblName); Assert.Equal(1660504, observed.Partner.Position); Assert.False(observed.Partner.OnReverseStrand); var observed2 = adjacencies[1]; Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed2.Origin.Chromosome.EnsemblName); Assert.Equal(1660504, observed2.Origin.Position); Assert.True(observed2.Origin.OnReverseStrand); Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed2.Partner.Chromosome.EnsemblName); Assert.Equal(1594583, observed2.Partner.Position); Assert.True(observed2.Partner.OnReverseStrand); }
public void CreateFromSymbolicAllele_Inversion() { var interval = new ChromosomeInterval(ChromosomeUtilities.Chr1, 63989116, 64291267); BreakEndAdjacency[] adjacencies = BreakEndUtilities.CreateFromSymbolicAllele(interval, VariantType.inversion); Assert.NotNull(adjacencies); Assert.Equal(2, adjacencies.Length); var observed = adjacencies[0]; Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed.Origin.Chromosome.EnsemblName); Assert.Equal(63989115, observed.Origin.Position); Assert.False(observed.Origin.OnReverseStrand); Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed.Partner.Chromosome.EnsemblName); Assert.Equal(64291267, observed.Partner.Position); Assert.True(observed.Partner.OnReverseStrand); var observed2 = adjacencies[1]; Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed2.Origin.Chromosome.EnsemblName); Assert.Equal(64291268, observed2.Origin.Position); Assert.True(observed2.Origin.OnReverseStrand); Assert.Equal(ChromosomeUtilities.Chr1.EnsemblName, observed2.Partner.Chromosome.EnsemblName); Assert.Equal(63989116, observed2.Partner.Position); Assert.False(observed2.Partner.OnReverseStrand); }
public void CreateFromSymbolicAllele_UnhandledVariantType_ReturnNull() { var interval = new ChromosomeInterval(ChromosomeUtilities.Chr1, 63989116, 64291267); BreakEndAdjacency[] adjacencies = BreakEndUtilities.CreateFromSymbolicAllele(interval, VariantType.complex_structural_alteration); Assert.Null(adjacencies); }
private static BreakEndAdjacency[] GetBreakEndAdjacencies(ISimpleVariant variant, IDictionary <string, IChromosome> refNameToChromosome) => variant.Type == VariantType.translocation_breakend ? BreakEndUtilities.CreateFromTranslocation(variant, refNameToChromosome) : BreakEndUtilities.CreateFromSymbolicAllele(variant, variant.Type);