public static bool IsDuplicateFailedQCLowQuality(BamAlignment alignment, uint qualityThreshold)
{
if (alignment.IsDuplicate()) { return true; }
if (alignment.IsFailedQC()) { return true; }
if (alignment.MapQuality == FragmentBinnerConstants.MappingQualityNotAvailable
|| alignment.MapQuality < qualityThreshold)
{
return true;
}
return false;
}