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 IWittyerBnd Create([NotNull] IVcfVariant first, [CanBeNull] IVcfSample originalSample,
[NotNull] WittyerType svType, [NotNull] IReadOnlyList <uint> bins, uint bpd, double?percentageDistance,
[NotNull] IVcfVariant second)
{
if (!ReferenceEquals(first, second))
{
(first, second) = FindBndEntriesOrder(in first, in second);
}
var ciPosInterval = first.Position.ConvertPositionToCiInterval(first, WittyerConstants.Cipos);
var ciEndInterval = ReferenceEquals(first, second)
? ciPosInterval // same variant means same intervals.
: second.Position.ConvertPositionToCiInterval(second, WittyerConstants.Cipos);
IContigAndInterval posInterval, endInterval;
if (ReferenceEquals(first, second)) // insertions need trimming and stuff.
{
var trimmed = first.TryNormalizeVariant(VariantNormalizer.TrimCommonBases, 0).GetOrThrow();
var tuple = (bpd, bpd);
var(posStart, posStop) = trimmed.Position.ConvertPositionToCiInterval(tuple);
WittyerUtils.GetBetterInterval(ciPosInterval, ref posStart, ref posStop);
posInterval = endInterval = ContigAndInterval.Create(first.Contig, posStart, posStop);
}
else
{
(posInterval, endInterval) = WittyerUtils.GetPosAndEndInterval(first.Contig,
svType == WittyerType.IntraChromosomeBreakend ? percentageDistance : null, bpd,
ciPosInterval, first.Position, ciEndInterval, second.Position, second.Contig);
}
var winner = GetWinner();
var sample = WittyerSample.CreateFromVariant(first, originalSample, false);
return(new WittyerBndInternal(svType, first, posInterval, ciPosInterval,
second, endInterval, ciEndInterval, winner, sample));
(IVcfVariant first, IVcfVariant second) FindBndEntriesOrder(in IVcfVariant variantA,
in IVcfVariant variantB)
=> ContigAndPositionComparer.Default.Compare(variantA, variantB) > 0
? (variantB, variantA)
: (variantA, variantB);
Winner GetWinner()
{
if (svType == WittyerType.TranslocationBreakend)
{
return(Winner.Create(svType));
}
IInterval <uint> bedInterval;
if (svType == WittyerType.Insertion)
{
bedInterval = GetInsertionInterval(first);
}
else
{
var start = first.Position;
if (start > 0)
{
start--;
}
bedInterval = BedInterval.Create(start, second.Position);
}
return(Winner.Create(svType, bedInterval, bins));
}
}
