private static VariantInfo GetVariantInfo(PositionSet positionSet, AlleleBlock alleleBlock)
{
var positions = positionSet.SimplePositions;
int startIndex = alleleBlock.PositionIndex;
int numPositions = alleleBlock.AlleleIndexes.Length;
int numSamples = positionSet.NumSamples;
string qual = GetStringWithMinValueOrDot(Enumerable.Range(startIndex, numPositions)
.Select(x => positions[x].VcfFields[VcfCommon.QualIndex]));
var filters = Enumerable.Range(startIndex, numPositions)
.Select(i => positions[i].VcfFields[VcfCommon.FilterIndex])
.ToArray();
var gqValues = new string[numSamples];
for (var i = 0; i < numSamples; i++)
{
gqValues[i] = GetStringWithMinValueOrDot(
new ArraySegment <string>(positionSet.GqInfo.Values[i], startIndex, numPositions).ToArray());
}
var psValues = new string[numSamples];
for (var i = 0; i < numSamples; i++)
{
var psTagsThisSample =
new ArraySegment <string>(positionSet.PsInfo.Values[i], startIndex, numPositions);
var isHomozygous = new ArraySegment <bool>(
positionSet.GtInfo.Values[i].Select(x => x.IsHomozygous).ToArray(), startIndex, numPositions);
psValues[i] = GetPhaseSetForRecomposedVariant(psTagsThisSample, isHomozygous);
}
var homoReferenceSamplePloidy = new int?[numSamples];
for (var i = 0; i < numSamples; i++)
{
if (Genotype.IsAllHomozygousReference(positionSet.GtInfo.Values[i], startIndex, numPositions))
{
homoReferenceSamplePloidy[i] = positionSet.GtInfo.Values[i][startIndex].AlleleIndexes.Length;
}
}
var sampleFilters = new List <bool> [numSamples];
for (var i = 0; i < numSamples; i++)
{
sampleFilters[i] = new List <bool>();
}
return(new VariantInfo(qual, filters, gqValues, psValues, homoReferenceSamplePloidy, sampleFilters));
}
