/// <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); }