internal static IWittyerVariant Create([NotNull] IVcfVariant baseVariant,
[CanBeNull] IVcfSample sample, [NotNull] WittyerType svType,
[NotNull] IReadOnlyList <uint> bins, [CanBeNull] double?percentageDistance,
uint basepairDistance)
{
// originalInterval is needed to adjust CIPOS and CIEND against for PD/BPD, but it won't be used for actual reflen and binning.
var baseInterval = baseVariant.ToBedInterval(true, out var originalEnd, out var sharedFirstBase);
if (baseInterval == null)
{
throw new InvalidOperationException(
$"Expected failure of {nameof(WittyerUtils.ToBedInterval)} to throw, but didn't...");
}
// CI intervals are always based on the original POS/END
var posStart = baseVariant.Position;
if (sharedFirstBase)
{
posStart++;
}
var ciPosInterval = posStart.ConvertPositionToCiInterval(baseVariant, WittyerConstants.Cipos);
var ciEndInterval = originalEnd.ConvertPositionToCiInterval(baseVariant, WittyerConstants.Ciend);
var baseStart = sharedFirstBase
? baseInterval.Start
: baseInterval.Start + 1; // not sharing first base (ref site or complex types, etc) need adjustment
// the pd/bpd intervals are based on the trimmed variant's coordinates.
var(posInterval, endInterval) = WittyerUtils.GetPosAndEndInterval(baseVariant.Contig, percentageDistance,
basepairDistance, ciPosInterval, baseStart, ciEndInterval, baseInterval.Stop);
return(new WittyerVariantInternal(svType, baseVariant, baseInterval,
Winner.Create(svType, baseInterval, bins),
posInterval, ciPosInterval, endInterval, ciEndInterval,
WittyerSample.CreateFromVariant(baseVariant, sample, svType == WittyerType.CopyNumberReference)));
}
internal static IInterval <uint> GetInsertionInterval([NotNull] IVcfVariant first)
=> first.IsAltSimpleSequence(0)
? first.ToBedInterval(false, out _, out _)
: first.TryGetSvLength(out var svLen) != null
