private static void UpdateWittyerVariant(IWittyerSimpleVariant variant, EvaluationMode emode, bool isTruth)
{
var sample = variant.Sample;
var match = emode.Equals(EvaluationMode.Default);
variant.OverlapInfo.Sort();
switch (sample)
{
case WittyerSampleInternal simple:
UpdateWittyerVariantHelper(simple, variant, match, isTruth);
break;
case WittyerCopyNumberSample cnsample:
UpdateWittyerVariantHelper(cnsample.BaseSample, variant, match, isTruth);
break;
case WittyerGenotypedSample gtSample:
UpdateWittyerVariantHelper(gtSample.BaseSample, variant, match, isTruth);
break;
case WittyerGenotypedCopyNumberSample gtCnSample:
UpdateWittyerVariantHelper(gtCnSample.BaseSample.BaseSample, variant, match, isTruth);
break;
default:
throw new InvalidDataException(
"Not sure how we get here, you must have created some non-existed wittyer sample type, check with developer!");
}
}
public static BorderDistance CreateFromVariant([NotNull] IWittyerSimpleVariant first,
[NotNull] IWittyerSimpleVariant second)
{
var lbl = GetDistance(first.CiPosInterval.Start, second.CiPosInterval.Start);
var lbr = GetDistance(first.CiPosInterval.Stop, second.CiPosInterval.Stop);
var rbl = GetDistance(first.CiEndInterval.Start, second.CiEndInterval.Start);
var rbr = GetDistance(first.CiEndInterval.Stop, second.CiEndInterval.Stop);
return(Create(lbl, lbr, rbl, rbr));
}
private static void UpdateWittyerVariantHelper(WittyerSampleInternal sample,
IWittyerSimpleVariant variant, bool isGenotypeMatch, bool isTruth)
{
var correctMatch = new [] { MatchEnum.AlleleAndGenotypeMatch }.ToList();
if (!isGenotypeMatch)
{
correctMatch.Add(MatchEnum.AlleleMatch);
}
sample.What = variant.OverlapInfo.Select(x => x.What).ToImmutableList();
if (variant.OverlapInfo.Count == 0)
{
sample.What = ImmutableList.Create(MatchEnum.Unmatched);
}
sample.Why = variant.OverlapInfo.Select(x => x.Why).ToImmutableList();
sample.Wit = correctMatch.Any(sample.What.Contains)
? WitDecision.TruePositive
: (isTruth ? WitDecision.FalseNegative : WitDecision.FalsePositive);
}
internal Builder AddQuery(IWittyerSimpleVariant variant)
{
_query = _query.Add(variant);
return this;
}
internal void AddVariantToTrees(IWittyerSimpleVariant variant)
{
var tree = _trees.GetOrAdd(variant.VariantType, GenomeIntervalTree <IWittyerSimpleVariant> .Create());
tree.Add(variant);
}