private void AddTranscripts(IAnnotatedPosition annotatedPosition)
{
var overlappingTranscripts = _transcriptCache.GetOverlappingFlankingTranscripts(annotatedPosition.Position);
if (overlappingTranscripts == null)
{
// todo: handle intergenic variants
return;
}
foreach (var annotatedVariant in annotatedPosition.AnnotatedVariants)
{
var annotatedTranscripts = new List <IAnnotatedTranscript>();
PianoAnnotationUtils.GetAnnotatedTranscripts(annotatedVariant.Variant, overlappingTranscripts,
_sequence, annotatedTranscripts);
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);
}
}
}
}
