internal static ISample[] ToSamples(this string[] vcfColumns, FormatIndices formatIndices, int numAltAlleles, bool isRepeatExpansion)
{
if (vcfColumns.Length < VcfCommon.MinNumColumnsSampleGenotypes)
{
return(null);
}
int numSamples = vcfColumns.Length - VcfCommon.MinNumColumnsSampleGenotypes + 1;
var samples = new ISample[numSamples];
formatIndices.Set(vcfColumns[VcfCommon.FormatIndex]);
for (int index = VcfCommon.GenotypeIndex; index < vcfColumns.Length; index++)
{
samples[index - VcfCommon.GenotypeIndex] = ExtractSample(vcfColumns[index], formatIndices, numAltAlleles, isRepeatExpansion);
}
return(samples);
}
internal static ISample[] ToSamples(this string[] vcfColumns, FormatIndices formatIndices, ISimplePosition simplePosition, IMitoHeteroplasmyProvider mitoHeteroplasmyProvider, bool enableDq = false)
{
if (vcfColumns.Length < VcfCommon.MinNumColumnsSampleGenotypes)
{
return(null);
}
int numSamples = vcfColumns.Length - VcfCommon.MinNumColumnsSampleGenotypes + 1;
var samples = new ISample[numSamples];
formatIndices.Set(vcfColumns[VcfCommon.FormatIndex]);
var legacySampleExtractor = IsLegacyVariantCaller(formatIndices) ? new LegacySampleFieldExtractor(vcfColumns, formatIndices) : null;
for (int index = VcfCommon.GenotypeIndex; index < vcfColumns.Length; index++)
{
samples[index - VcfCommon.GenotypeIndex] = ExtractSample(vcfColumns[index], formatIndices, simplePosition, mitoHeteroplasmyProvider, legacySampleExtractor, enableDq);
}
return(samples);
}
internal static ISample[] ToSamples(this string[] vcfColumns, FormatIndices formatIndices, int numAltAlleles)
{
if (vcfColumns.Length < VcfCommon.MinNumColumnsSampleGenotypes)
{
return(null);
}
int numSamples = vcfColumns.Length - VcfCommon.MinNumColumnsSampleGenotypes + 1;
var samples = new ISample[numSamples];
formatIndices.Set(vcfColumns[VcfCommon.FormatIndex]);
var legacySampleExtractor = IsLegacyVariantCaller(formatIndices) ? new LegacySampleFieldExtractor(vcfColumns, formatIndices) : null;
for (int index = VcfCommon.GenotypeIndex; index < vcfColumns.Length; index++)
{
samples[index - VcfCommon.GenotypeIndex] = ExtractSample(vcfColumns[index], formatIndices, numAltAlleles, legacySampleExtractor);
}
return(samples);
}
