internal static IInterval <uint> ToBedInterval([NotNull] this IVcfVariant baseVariant,
bool throwException, out uint endVal, out bool sharedFirstBase)
{
endVal = baseVariant.Position;
if (IsSimpleSequence(baseVariant,
out var refLenVal, out sharedFirstBase, out var sharedLastBase, false))
// first need to save the original end before normalizing
{
endVal += refLenVal;
if (baseVariant.Alts.Count > 0) // refsites don't have Alts in VariantUtils
{
baseVariant = baseVariant.TryNormalizeVariant(VariantNormalizer.TrimCommonBases, 0).GetOrThrow();
}
}
var refLen = baseVariant.GetSvLength(throwException, out sharedFirstBase, out sharedLastBase, out var endPos);
if (refLen == null) // means insertion of unknown length.
{
return(null);
}
if (endPos != null)
{
endVal = endPos.Value;
}
var start = sharedFirstBase || baseVariant.Position == 0 ? baseVariant.Position : baseVariant.Position - 1;
var end = start + refLen.Value;
if (sharedLastBase) // rare case
{
end--;
}
return(BedInterval.Create(start, end));
}
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));
}
}
