public static int GetPloidy(PloidyInfo referencePloidy, string chrom, int start, int end, int defaultPloidy = 2)
{
if (referencePloidy == null)
{
return(defaultPloidy);
}
CanvasSegment segment = new CanvasSegment(chrom, start, end, new List <float>());
return(referencePloidy.GetReferenceCopyNumber(segment));
}
private bool IsPassVariant(CanvasSegment segment, PloidyInfo ploidyInfo)
{
if (!segment.Filter.IsPass)
{
return(false);
}
var referenceCopyNumber = ploidyInfo?.GetReferenceCopyNumber(segment) ?? 2;
if (segment.CopyNumber != referenceCopyNumber)
{
return(true);
}
if (segment.CopyNumber == 2 && segment.MajorChromosomeCount == 2)
{
return(true); //LOH
}
return(false);
}