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 WittyerVariantInternal Create([NotNull] IVcfVariant baseVariant,
IInterval <uint> baseInterval,
WittyerVariantType svType,
IContigAndInterval startInterval, Winner win,
List <OverlapAnnotation> overlapInfo, IWittyerSample sample, IContigAndInterval endInterval)
=> new WittyerVariantInternal(baseVariant, baseInterval, svType, startInterval, win,
overlapInfo, sample, endInterval);
private WittyerBndInternal([NotNull] IVcfVariant baseVariant, IInterval <uint> posInterval, Winner win,
IContigAndInterval endInterval,
List <OverlapAnnotation> overlapInfo, IWittyerSample sample, IVcfVariant endOriginalVariant, WittyerVariantType svType)
{
Contig = baseVariant.Contig;
_posInterval = posInterval;
EndInterval = endInterval;
OverlapInfo = overlapInfo;
Sample = sample;
OriginalVariant = baseVariant;
EndOriginalVariant = endOriginalVariant;
Win = win;
VariantType = svType;
}
private WittyerVariantInternal([NotNull] IVcfVariant baseVariant, IInterval <uint> baseInterval,
WittyerVariantType svType,
IContigAndInterval posInterval, Winner win,
List <OverlapAnnotation> overlapInfo, IWittyerSample sample, IContigAndInterval endInterval)
{
OriginalVariant = baseVariant;
Contig = baseVariant.Contig;
VariantType = svType;
Win = win;
OverlapInfo = overlapInfo;
Sample = sample;
_baseInterval = baseInterval;
PosInterval = posInterval;
EndInterval = endInterval;
}
internal static IWittyerBnd Create([NotNull] IVcfVariant baseVariant, IInterval <uint> posInterval,
Winner win, IContigAndInterval endInterval, List <OverlapAnnotation> overlapInfo,
IWittyerSample sample, IVcfVariant endOriginalVariant, WittyerVariantType svType)
=> new WittyerBndInternal(baseVariant, posInterval, win, endInterval, overlapInfo, sample,
endOriginalVariant, svType);
