public void Elongation(VariantType variantType, OverlapType overlapType, EndpointOverlapType endpointOverlapType, bool expectedResult)
{
var featureEffect = new FeatureVariantEffects(overlapType, endpointOverlapType, false, variantType, true);
bool observedResult = featureEffect.Elongation();
Assert.Equal(expectedResult, observedResult);
}
private static List <ConsequenceTag> GetConsequences(IInterval transcript, IVariant variant)
{
var featureEffect = new FeatureVariantEffects(transcript, variant.Type, variant, true);
var consequence = new Consequences(null, featureEffect);
consequence.DetermineStructuralVariantEffect(variant);
return(consequence.GetConsequences());
}
public void FivePrimeDuplicatedTranscript(VariantType variantType, OverlapType overlapType, EndpointOverlapType endpointOverlapType,
bool onReverseStrand, bool expectedResult)
{
var featureEffect = new FeatureVariantEffects(overlapType, endpointOverlapType, onReverseStrand, variantType, true);
bool observedResult = featureEffect.FivePrimeDuplicatedTranscript();
Assert.Equal(expectedResult, observedResult);
}
public static IAnnotatedRegulatoryRegion Annotate(IVariant variant, IRegulatoryRegion regulatoryRegion)
{
var featureEffect = new FeatureVariantEffects(regulatoryRegion, variant.Type, variant, variant.IsStructuralVariant);
var consequence = new Consequences(null, featureEffect);
consequence.DetermineRegulatoryVariantEffects();
return(new AnnotatedRegulatoryRegion(regulatoryRegion, consequence.GetConsequences()));
}
private static IEnumerable <ConsequenceTag> GetConsequences(IInterval transcript, ISimpleVariant variant,
bool hasGeneFusionAnnotation)
{
var featureEffect = new FeatureVariantEffects(transcript, variant.Type, variant, true);
var consequence = new Consequences(null, featureEffect);
consequence.DetermineStructuralVariantEffect(variant.Type, hasGeneFusionAnnotation);
return(consequence.GetConsequences());
}
private static List <ConsequenceTag> GetConsequences(ITranscript transcript, IVariant variant, VariantEffect variantEffect)
{
var featureEffect = new FeatureVariantEffects(transcript, variant.Type, variant.Start, variant.End,
variant.Behavior.StructuralVariantConsequence);
var consequence = new Consequences(variantEffect, featureEffect);
consequence.DetermineSmallVariantEffects();
return(consequence.GetConsequences());
}
private static List <ConsequenceTag> GetConsequences(IInterval transcript, bool onReverseStrand, IVariant variant)
{
OverlapType overlapType = Intervals.Utilities.GetOverlapType(transcript.Start, transcript.End, variant.Start, variant.End);
EndpointOverlapType endpointOverlapType = Intervals.Utilities.GetEndpointOverlapType(transcript.Start, transcript.End, variant.Start, variant.End);
var featureEffect = new FeatureVariantEffects(overlapType, endpointOverlapType, onReverseStrand, variant.Type, true);
var consequence = new Consequences(variant.Type, null, featureEffect);
consequence.DetermineStructuralVariantEffect(variant);
return(consequence.GetConsequences());
}
public static IAnnotatedRegulatoryRegion Annotate(IVariant variant, IRegulatoryRegion regulatoryRegion)
{
OverlapType overlapType = Intervals.Utilities.GetOverlapType(regulatoryRegion.Start, regulatoryRegion.End,
variant.Start, variant.End);
EndpointOverlapType endpointOverlapType =
Intervals.Utilities.GetEndpointOverlapType(regulatoryRegion.Start, regulatoryRegion.End, variant.Start, variant.End);
var featureEffect = new FeatureVariantEffects(overlapType, endpointOverlapType, false, variant.Type, variant.IsStructuralVariant);
var consequence = new Consequences(VariantType.unknown, null, featureEffect);
consequence.DetermineRegulatoryVariantEffects();
return(new AnnotatedRegulatoryRegion(regulatoryRegion, consequence.GetConsequences()));
}
public void Elongation(VariantType variantType, int variantStart, int variantEnd, bool expectedResult)
{
var featureEffect = new FeatureVariantEffects(new Interval(150, 250), variantType, new Interval(variantStart, variantEnd), true);
Assert.Equal(expectedResult, featureEffect.Elongation());
}
public void Not_Ablation_if_not_completely_overlapped(int variantStart, int variantEnd, bool expectedResult)
{
var featureEffect = new FeatureVariantEffects(new Interval(150, 250), VariantType.deletion, new Interval(variantStart, variantEnd), false);
Assert.Equal(expectedResult, featureEffect.Ablation());
}
public void Ablation(VariantType type, bool expectResult)
{
var featureEffect = new FeatureVariantEffects(new Interval(100, 200), type, new Interval(50, 300), true);
Assert.Equal(expectResult, featureEffect.Ablation());
}
