private static List <(string, int)> GetGenotypesAndStarts(PositionSet positionSet, int sampleIndex)
{
var genotypesAndStartIndexes = new List <(string, int)>();
var gtTags = new List <string>();
int startIndexInBlock = 0;
string previousPhaseSetId = null;
for (var i = 0; i < positionSet._numPositions; i++)
{
var thisSampleInfo = positionSet._sampleInfo[i, sampleIndex];
string currentPhaseSetId = positionSet.PsInfo[sampleIndex][i];
if (previousPhaseSetId == null)
{
// ReSharper disable once RedundantAssignment
previousPhaseSetId = currentPhaseSetId;
}
else if (currentPhaseSetId != previousPhaseSetId)
{
if (gtTags.Count > 1)
{
genotypesAndStartIndexes.Add((string.Join(";", gtTags), startIndexInBlock));
}
gtTags = new List <string>();
startIndexInBlock = i;
}
gtTags.Add(thisSampleInfo[0]);
previousPhaseSetId = currentPhaseSetId;
}
if (gtTags.Count > 1)
{
genotypesAndStartIndexes.Add((string.Join(";", gtTags), startIndexInBlock));
}
return(genotypesAndStartIndexes);
}
private static string[, ][] GetSampleInfo(PositionSet positionSet)
{
var sampleInfo = new String[positionSet._numPositions, positionSet.NumSamples][];
for (var i = 0; i < positionSet._numPositions; i++)
{
for (int sampleIndex = 0; sampleIndex < positionSet.NumSamples; sampleIndex++)
{
int sampleColIndex = sampleIndex + VcfCommon.GenotypeIndex;
sampleInfo[i, sampleIndex] = positionSet.SimplePositions[i].VcfFields[sampleColIndex].Split(":");
}
}
return(sampleInfo);
}
private static AlleleSet GenerateAlleleSet(PositionSet positionSet)
{
var alleleArrays = new string[positionSet._numPositions][];
var starts = positionSet.SimplePositions.Select(x => x.Start).ToArray();
for (int index = 0; index < positionSet._numPositions; index++)
{
var position = positionSet.SimplePositions[index];
alleleArrays[index] = new string[position.AltAlleles.Length + 1];
alleleArrays[index][0] = position.RefAllele;
position.AltAlleles.CopyTo(alleleArrays[index], 1);
}
return(new AlleleSet(positionSet.SimplePositions[0].Chromosome, starts, alleleArrays));
}
public static PositionSet CreatePositionSet(List <ISimplePosition> simpleSimplePositions, List <int> functionBlockRanges)
{
var positionSet = new PositionSet(simpleSimplePositions, functionBlockRanges);
positionSet.AlleleSet = GenerateAlleleSet(positionSet);
positionSet._allelesWithUnsupportedTypes = GetAllelesWithUnsupportedTypes(positionSet);
positionSet._sampleInfo = GetSampleInfo(positionSet);
var phaseSetAndGqIndexes = positionSet.GetSampleTagIndexes(new[] { "PS", "GQ" });
positionSet.PsInfo = GetTagInfo(positionSet._sampleInfo, phaseSetAndGqIndexes[0], ExtractSamplePhaseSet);
positionSet.GqInfo = GetTagInfo(positionSet._sampleInfo, phaseSetAndGqIndexes[1], ExtractSampleGq);
var genotypeToSampleIndex = GetGenotypeToSampleIndex(positionSet);
positionSet.AlleleIndexBlockToSampleIndex = AlleleIndexBlock.GetAlleleIndexBlockToSampleIndex(genotypeToSampleIndex, positionSet._allelesWithUnsupportedTypes, positionSet.AlleleSet.Starts, positionSet.FunctionBlockRanges);
return(positionSet);
}
private static HashSet <string>[] GetAllelesWithUnsupportedTypes(PositionSet positionSet)
{
var allelesWithUnsupportedTypes = new HashSet <string> [positionSet._numPositions];
for (int posIndex = 0; posIndex < positionSet._numPositions; posIndex++)
{
allelesWithUnsupportedTypes[posIndex] = new HashSet <string>();
var thisPosition = positionSet.SimplePositions[posIndex];
for (int varIndex = 0; varIndex < thisPosition.AltAlleles.Length; varIndex++)
{
if (!(IsSupportedVariantType(thisPosition.RefAllele, thisPosition.AltAlleles[varIndex]) || thisPosition.VcfFields[VcfCommon.AltIndex] == VcfCommon.GatkNonRefAllele)) //todo: simplify the logic
{
allelesWithUnsupportedTypes[posIndex].Add((varIndex + 1).ToString()); // GT tag is 1-based
}
}
}
return(allelesWithUnsupportedTypes);
}
private static Dictionary <(string Genotypes, int Start), List <int> > GetGenotypeToSampleIndex(PositionSet positionSet)
{
var genotypeToSample = new Dictionary <(string, int), List <int> >();
for (int sampleIndex = 0; sampleIndex < positionSet.NumSamples; sampleIndex++)
{
var genotypesAndStartIndexes = GetGenotypesAndStarts(positionSet, sampleIndex);
foreach (var genotypeAndSartIndex in genotypesAndStartIndexes)
{
if (genotypeToSample.ContainsKey(genotypeAndSartIndex))
{
genotypeToSample[genotypeAndSartIndex].Add(sampleIndex);
}
else
{
genotypeToSample[genotypeAndSartIndex] = new List <int> {
sampleIndex
}
};
}
}
return(genotypeToSample);
}
