private static void AddFormatAndSampleColumns(List <int>[] sampleGenoTypes, VariantInfo variantInfo, ref List <string> vcfFields)
{
var formatTags = "GT";
var hasGq = false;
var hasPs = false;
int numSamples = sampleGenoTypes.Length;
string[] sampleGenotypeStrings = GetSampleGenotypeStrings(sampleGenoTypes, variantInfo, ref hasGq, ref hasPs, numSamples);
int numFields = 1;
if (hasGq)
{
formatTags += ":GQ";
numFields++;
}
if (hasPs)
{
formatTags += ":PS";
numFields++;
}
vcfFields.Add(formatTags);
for (var index = 0; index < numSamples; index++)
{
string sampleGenotypeStr = sampleGenotypeStrings[index];
if (sampleGenotypeStr == null || sampleGenotypeStr == ".")
{
vcfFields.Add(".");
}
else
{
var nonMissingFields = new string[numFields];
nonMissingFields[0] = sampleGenotypeStr;
var fieldIndex = 1;
if (hasGq)
{
nonMissingFields[fieldIndex] = variantInfo.SampleGqs[index];
fieldIndex++;
}
if (hasPs)
{
nonMissingFields[fieldIndex] = variantInfo.SamplePhaseSets[index];
}
var sampleColumnStr = string.Join(":", TrimTrailingMissValues(nonMissingFields));
vcfFields.Add(sampleColumnStr);
}
}
}
private string[] GetVcfFields(VariantSite varSite, VariantInfo variantInfo, string altAlleleColumn, List <int>[] sampleGenoTypes, string variantId = VariantId, string info = InfoTag)
{
var vcfFields = new List <string>
{
_chrName,
varSite.Start.ToString(),
variantId,
varSite.RefAllele,
altAlleleColumn,
variantInfo.Qual,
variantInfo.GetMnvFilterTag(),
info
};
AddFormatAndSampleColumns(sampleGenoTypes, variantInfo, ref vcfFields);
return(vcfFields.ToArray());
}
private static string[] GetSampleGenotypeStrings(IReadOnlyList <List <int> > sampleGenoTypes, VariantInfo variantInfo, ref bool hasGq, ref bool hasPs, int numSamples)
{
var sampleGenotypeStrings = new string[numSamples];
for (var index = 0; index < numSamples; index++)
{
var homoReferenceSamplePloidy = variantInfo.HomoReferenceSamplePloidies[index];
sampleGenotypeStrings[index] = GetGenotype(sampleGenoTypes[index], homoReferenceSamplePloidy);
if (sampleGenotypeStrings[index] == ".")
{
continue;
}
if (variantInfo.SampleGqs[index] != ".")
{
hasGq = true;
}
if (variantInfo.SamplePhaseSets[index] != ".")
{
hasPs = true;
}
}
return(sampleGenotypeStrings);
}
