public static IWittyerSample CreateFromVariant(IVcfVariant baseVariant, [CanBeNull] IVcfSample sample, bool isReference)
{
if (isReference)
{
return(CreateReferenceSample(baseVariant, sample));
}
if (sample == null)
{
return(WittyerSampleInternal.Create(null));
}
var wittyerSample = WittyerSampleInternal.Create(sample);
var hasGt = sample.SampleDictionary.ContainsKey(VcfConstants.GenotypeKey);
if (!sample.SampleDictionary.TryGetValue(VcfConstants.CnSampleFieldKey, out var cnString))
{
return(hasGt
? WittyerGenotypedSample.Create(wittyerSample, GenotypeInfo.CreateFromSample(sample))
as IWittyerSample
: wittyerSample);
}
uint?cnNumber;
if (cnString == VcfConstants.MissingValueString)
{
cnNumber = null;
}
else if (uint.TryParse(cnString, out var cnNumberLocal))
{
cnNumber = cnNumberLocal;
}
else
{
throw new InvalidDataException($"{VcfConstants.CnSampleFieldKey} does not have a valid value in {baseVariant}");
}
var cnSample = WittyerCopyNumberSample.Create(wittyerSample, cnNumber);
if (!hasGt)
{
return(cnSample);
}
var gtInfo = GenotypeInfo.CreateFromSample(sample);
return(WittyerGenotypedCopyNumberSample.Create(cnSample, gtInfo));
}
internal static IWittyerGenotypedCopyNumberSample CreateReferenceSample([NotNull] IVcfVariant baseVariant, [CanBeNull] IVcfSample sample)
{
var ploidy = 2;
if (sample == null)
{
return(WittyerGenotypedCopyNumberSample.Create(
WittyerCopyNumberSample.Create(WittyerSampleInternal.Create(null), (uint)ploidy),
GenotypeInfo.CreateRef(ploidy, false)));
}
var isPhased = false;
if (sample.SampleDictionary.TryGetValue(VcfConstants.GenotypeKey, out var originalGt))
{
isPhased = originalGt.Contains(VcfConstants.GtPhasedValueDelimiter);
ploidy = originalGt
.Split(isPhased ? VcfConstants.GtPhasedValueDelimiter : VcfConstants.GtUnphasedValueDelimiter).Length;
}
var cnSample = WittyerCopyNumberSample.Create(WittyerSampleInternal.Create(sample), (uint)ploidy);
return(WittyerGenotypedCopyNumberSample.Create(cnSample, GenotypeInfo.CreateRef(ploidy, isPhased)));
}