// constructor
public IntermediateSampleFields(string[] vcfColumns, FormatIndices formatIndices, string[] sampleCols, bool fixGatkGenomeVcf = false)
{
VcfRefAllele = vcfColumns[VcfCommon.RefIndex];
FormatIndices = formatIndices;
SampleColumns = sampleCols;
if (formatIndices.MCC != null)
{
MajorChromosomeCount = int.Parse(sampleCols[formatIndices.MCC.Value]);
}
if (formatIndices.CN != null)
{
CopyNumber = int.Parse(sampleCols[formatIndices.CN.Value]);
}
if (fixGatkGenomeVcf && formatIndices.AD != null)
{
sampleCols[formatIndices.AD.Value] = CorrectAdInGatkGenomeVcf(sampleCols[formatIndices.AD.Value]);
}
if (formatIndices.DQ != null)
{
DenovoQuality = GetDenovoQuality(sampleCols[formatIndices.DQ.Value]);
}
AltAlleles = vcfColumns[VcfCommon.AltIndex].Split(',');
CalculateTirTar();
CalculateRawAlleleCounts();
GetPlatypusCounts();
}
/// <summary>
/// extracts the genotype fields from the VCF file and returns a list of JSON samples
/// </summary>
internal List <JsonSample> ExtractSamples(bool fixGatkGenomeVcf = false)
{
// sanity check: make sure we have enough columns
if (_vcfColumns.Length < VcfCommon.MinNumColumnsSampleGenotypes)
{
return(null);
}
var samples = new List <JsonSample>();
// extract the indices for each genotype field
_formatIndices = FormatIndices.Extract(_vcfColumns[VcfCommon.FormatIndex]);
// add each sample
for (var index = VcfCommon.GenotypeIndex; index < _vcfColumns.Length; index++)
{
samples.Add(ExtractSample(_vcfColumns[index], fixGatkGenomeVcf));
}
return(samples);
}
