internal static IWittyerVariant Create([NotNull] IVcfVariant baseVariant,
string sample, double percentageDistance, uint basepairDistance,
IReadOnlyList <uint> bins, WittyerVariantType svType)
{
if (svType == WittyerVariantType.Invalid)
{
throw new InvalidDataException(
$"Invalid {VcfConstants.SvTypeKey} in variant: \n{baseVariant}\nNot sure why you got here though. Check with a witty.er developer!");
}
var end = baseVariant.Position + baseVariant.GetSvLength();
var baseInterval = BedInterval.Create(baseVariant.Position, end);
var borderInterval =
baseVariant.Position.CalculateBorderInterval(baseInterval,
baseVariant.ParseCi(WittyerConstants.Cipos),
percentageDistance, basepairDistance);
// wittyerVariant should all have end border, it's a matter of how to find it,
// either END key in INFO field, sort out through SVLEN or other ways, details can be defined in FindEndBorder() later
var endInterval = (end - 1).CalculateBorderInterval(baseInterval,
baseVariant.ParseCi(WittyerConstants.Ciend),
percentageDistance, basepairDistance);
var posContigAndInterval =
ContigAndInterval.Create(baseVariant.Contig, borderInterval.Start, borderInterval.Stop + 1);
var endContigAndInterval =
ContigAndInterval.Create(baseVariant.Contig, endInterval.Start, endInterval.Stop + 1);
return(Create(baseVariant, baseInterval, svType, posContigAndInterval,
Winner.Create(svType, baseInterval, bins), new List <OverlapAnnotation>(),
WittyerSample.CreateOverall(baseVariant, sample, svType == WittyerVariantType.CopyNumberReference),
endContigAndInterval));
}
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));
}
