public void GetOverlappingFlankingTranscripts_TwoOverlaps()
{
var interval = new Mock <IChromosomeInterval>();
interval.SetupGet(x => x.Chromosome).Returns(_chr1);
interval.SetupGet(x => x.Start).Returns(100);
interval.SetupGet(x => x.End).Returns(200);
var overlappingTranscripts = _cache.GetOverlappingTranscripts(interval.Object);
Assert.NotNull(overlappingTranscripts);
Assert.Equal(2, overlappingTranscripts.Length);
}
private void AddTranscripts(IAnnotatedPosition annotatedPosition)
{
var overlappingTranscripts = _transcriptCache.GetOverlappingTranscripts(annotatedPosition.Position);
if (overlappingTranscripts == null)
{
return;
}
foreach (var annotatedVariant in annotatedPosition.AnnotatedVariants)
{
var geneFusionCandidates = GetGeneFusionCandiates(annotatedVariant.Variant.BreakEnds);
var annotatedTranscripts = new List <IAnnotatedTranscript>();
TranscriptAnnotationFactory.GetAnnotatedTranscripts(annotatedVariant.Variant, overlappingTranscripts,
_sequence, annotatedTranscripts, annotatedVariant.OverlappingGenes,
annotatedVariant.OverlappingTranscripts, _siftCache, _polyphenCache, geneFusionCandidates);
if (annotatedTranscripts.Count == 0)
{
continue;
}
foreach (var annotatedTranscript in annotatedTranscripts)
{
if (annotatedTranscript.Transcript.Source == Source.Ensembl)
{
annotatedVariant.EnsemblTranscripts.Add(annotatedTranscript);
}
else
{
annotatedVariant.RefSeqTranscripts.Add(annotatedTranscript);
}
}
}
}
