public void RefMinorSite_have_correct_behavior()
{
var chrom = new Mock <IChromosome>();
chrom.Setup(x => x.EnsemblName).Returns("1");
var variant = ReferenceVariantCreator.Create(chrom.Object, 100, 100, "A", ".", "T");
Assert.True(variant.IsRefMinor);
Assert.NotNull(variant.Behavior);
Assert.True(variant.Behavior.NeedFlankingTranscript);
Assert.True(variant.Behavior.NeedSaPosition);
Assert.False(variant.Behavior.NeedSaInterval);
Assert.False(variant.Behavior.ReducedTranscriptAnnotation);
Assert.False(variant.Behavior.StructuralVariantConsequence);
var variant2 = ReferenceVariantCreator.Create(chrom.Object, 101, 101, "A", ".", null);
Assert.False(variant2.IsRefMinor);
Assert.Null(variant2.Behavior);
var variant3 = ReferenceVariantCreator.Create(chrom.Object, 100, 110, "A", ".", null);
Assert.False(variant3.IsRefMinor);
Assert.Null(variant3.Behavior);
}
public void ReferenceVariant_have_annotationBehaviorNull()
{
var chrom = new Mock <IChromosome>();
chrom.Setup(x => x.EnsemblName).Returns("1");
var variant = ReferenceVariantCreator.Create(chrom.Object, 100, 101, "A", ".", null);
Assert.False(variant.IsRefMinor);
Assert.Null(variant.Behavior);
}
public void Create_MultiplePositions_HasGlobalMajorAllele_ReturnNull()
{
IVariant[] variants = ReferenceVariantCreator.Create(_vidCreator, Sequence, ChromosomeUtilities.Chr1, 100, 101, "A", ".", "T");
Assert.Null(variants);
}
private IVariant GetVariant(int start, int end, string refAllele, string altAllele, string globalMajorAllele)
{
IVariant[] variants = ReferenceVariantCreator.Create(_vidCreator, Sequence, ChromosomeUtilities.Chr1, start, end, refAllele, altAllele, globalMajorAllele);
Assert.Single(variants);
return(variants[0]);
}
public void Create_SinglePosition_NoGlobalMajorAllele_ReturnNull()
{
IVariant[] variants = ReferenceVariantCreator.Create(_vidCreator, Sequence, ChromosomeUtilities.Chr1, 100, 100, "A", ".", null);
Assert.Null(variants);
}