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);
