internal static WittyerVariantType ParseWittyerVariantType([NotNull] this IVcfVariant variant,
[CanBeNull] string sampleName)
{
if (variant.IsRefCall(sampleName))
{
return(WittyerVariantType.CopyNumberReference);
}
//anything NOT a refcall requires SVTYPE INFO key
if (!variant.Info.TryGetValue(VcfConstants.SvTypeKey, out var svTypeStr))
{
throw new InvalidDataException(
$"Following variant does not have {VcfConstants.SvTypeKey} info key:\n{variant}");
}
if (TryParseEnumOrDescription(svTypeStr, out WittyerVariantType svType))
{
if (variant.Samples.Count > 0 &&
variant.Samples[0].SampleDictionary.ContainsKey(VcfConstants.CnSampleFieldKey) &&
WittyerConstants.BaseLevelStatsTypes.Contains(svType))
{
return(WittyerVariantType.Cnv);
}
return(svType);
}
if (!TryParseEnumOrDescription(svTypeStr, out SvType type) ||
!type.Equals(SvType.TranslocationBreakend))
{
throw new InvalidDataException($"Cannot recognize {svTypeStr}");
}
var bnd = variant as IGeneralBnd ?? GeneralBnd.Create(variant);
return(!bnd.Contig.Equals(bnd.Mate.Contig)
? WittyerVariantType.TranslocationBreakend
: WittyerVariantType.IntraChromosomeBreakend);
}
