public void When_needFlankingTranscript_flankingTranscript_get_flankingAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 100),
new Interval(102, 305), new AnnotationBehavior(false, true, false, true, false, false), new Interval(102, 305));
Assert.Equal(TranscriptAnnotationFactory.Status.FlankingAnnotation, observedStatus);
}
public void When_reducedTranscriptAnnotation_and_transcript_completely_overlapped_variant_but_gene_partial_overlap_get_reducedAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), new AnnotationBehavior(false, true, true, false, false, false), new Interval(102, 503));
Assert.Equal(TranscriptAnnotationFactory.Status.ReducedAnnotation, observedStatus);
}
public void When_not_reducedTranscriptAnnotation_partially_overlapped_variant_get_full_annotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 105),
new Interval(102, 305), new AnnotationBehavior(false, true, false, false, false, false), new Interval(102, 305));
Assert.Equal(TranscriptAnnotationFactory.Status.FullAnnotation, observedStatus);
}
public void NonOverlap_transcript_get_no_annotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 101),
new Interval(5102, 6100), new AnnotationBehavior(true, false, false, true, false, false), new Interval(5102, 6100));
Assert.Equal(TranscriptAnnotationFactory.Status.NoAnnotation, observedStatus);
}
public void When_reducedTranscriptAnnotation_and_gene_is_completely_overlapped_with_variant_get_SvCompleteOverlapAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), new AnnotationBehavior(false, true, true, false, false, false), new Interval(102, 305));
Assert.Equal(TranscriptAnnotationFactory.Status.SvCompleteOverlapAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Full_CompleteOverlap_ReturnFullAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), AnnotationBehavior.SmallVariants, Chromosome.ShortFlankingLength);
Assert.Equal(TranscriptAnnotationFactory.Status.FullAnnotation, observedStatus);
}
public void DecideAnnotationStatus_ROH_Return_RohAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), AnnotationBehavior.RunsOfHomozygosity, Chromosome.ShortFlankingLength);
Assert.Equal(TranscriptAnnotationFactory.Status.RohAnnotation, observedStatus);
}
public void DecideAnnotationStatus_NoOverlap_ReturnNoAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 101),
new Interval(5102, 6100), AnnotationBehavior.SmallVariants, Chromosome.ShortFlankingLength);
Assert.Equal(TranscriptAnnotationFactory.Status.NoAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Reduced_TranscriptPartialOverlap_ReturnReducedAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 200),
new Interval(102, 305), AnnotationBehavior.StructuralVariants, Chromosome.ShortFlankingLength);
Assert.Equal(TranscriptAnnotationFactory.Status.ReducedAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Full_PartialOverlap_ReturnFullAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 105),
new Interval(102, 305), AnnotationBehavior.SmallVariants);
Assert.Equal(TranscriptAnnotationFactory.Status.FullAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Flanking_ReturnFlankingAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 100),
new Interval(102, 305), AnnotationBehavior.SmallVariants);
Assert.Equal(TranscriptAnnotationFactory.Status.FlankingAnnotation, observedStatus);
}
public void DecideAnnotationStatus_ROH_Return_RohAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), AnnotationBehavior.RohBehavior);
Assert.Equal(TranscriptAnnotationFactory.Status.RohAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Full_CompleteOverlap_ReturnFullAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 500),
new Interval(102, 305), new AnnotationBehavior(false, true, false, false, false));
Assert.Equal(TranscriptAnnotationFactory.Status.FullAnnotation, observedStatus);
}
public void DecideAnnotationStatus_Reduced_TranscriptPartialOverlap_ReturnReducedAnnotation()
{
var observedStatus = TranscriptAnnotationFactory.DecideAnnotationStatus(new Interval(100, 200),
new Interval(102, 305), new AnnotationBehavior(false, true, true, false, false));
Assert.Equal(TranscriptAnnotationFactory.Status.ReducedAnnotation, observedStatus);
}