/// <summary>
/// checks if the variant is a reference no-call and sets the flag accordingly
/// </summary>
public static void Check(VariantFeature variant, bool limitToTranscript,
IIntervalForest <Transcript> transcriptIntervals)
{
// make sure we enabled reference no-call checking and that this is a reference site
if (!variant.IsReference)
{
return;
}
// make sure the filters failed
if (variant.PassFilter())
{
return;
}
if (!limitToTranscript)
{
variant.IsRefNoCall = true;
return;
}
// check if the variant overlaps any transcripts
variant.IsRefNoCall = transcriptIntervals.OverlapsAny(variant.ReferenceIndex, variant.OverlapReferenceBegin,
variant.OverlapReferenceEnd);
}
public void AssignCytogeneticBand(VariantFeature variant)
{
var cytogeneticBands = _compressedSequence.CytogeneticBands;
if (cytogeneticBands == null)
{
return;
}
variant.CytogeneticBand = cytogeneticBands.GetCytogeneticBand(variant.ReferenceIndex,
variant.VcfReferenceBegin, variant.VcfReferenceEnd);
}