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);
}
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);