// GenotypeBlocks can be shared by multiple samples
// We mainly utilize phase set information at this step to avoid duplicated calculation
// These GenotypeBlocks could be further segmented when more details considered
private static IEnumerable <GenotypeBlock> GetGenotypeBlocks(PositionSet positionSet, int sampleIndex)
{
var genotypes = positionSet.GtInfo.Values[sampleIndex];
var entireBlock = new GenotypeBlock(genotypes);
var blockRanges = GetGenotypeBlockRange(positionSet.PsInfo.Values[sampleIndex], genotypes.Select(x => x.IsPhased).ToArray(), genotypes.Select(x => x.IsHomozygous).ToArray());
var genotypeBlocks = new List <GenotypeBlock>();
foreach (var range in blockRanges)
{
genotypeBlocks.Add(entireBlock.GetSubBlock(range.StartIndex, range.PositionCount));
}
return(genotypeBlocks);
}
private static void AddAlleleIndexBlocks(GenotypeBlock genotypeBlock, List <int> sampleIndexes, int[] starts,
List <int> functionBlockRanges, IDictionary <AlleleBlock, List <SampleHaplotype> > alleleIndexBlockToSampleAllele, Graph <AlleleBlock> alleleIndexBlockGraph)
{
int startPosition = genotypeBlock.PosIndex;
int ploidy = genotypeBlock.Genotypes[0].AlleleIndexes.Length;
var isRefPositions = genotypeBlock.Genotypes.Select(x => IsRefPosition(x.AlleleIndexes)).ToArray();
foreach (var functionBlock in genotypeBlock.Split(starts, functionBlockRanges))
{
int startInThisBlock = functionBlock.PosIndex - startPosition;
int numPositions = functionBlock.Genotypes.Length;
int endInThisBlock = startInThisBlock + numPositions - 1;
var(numRefPosBefore, numRefPosAfter) = GetRefPosNums(isRefPositions, startInThisBlock, endInThisBlock);
var alleleIndexBlocks = new List <AlleleBlock>();
for (int haplotypeIndex = 0; haplotypeIndex < ploidy; haplotypeIndex++)
{
var alleleIndexes = new int[numPositions];
for (var i = 0; i < numPositions; i++)
{
alleleIndexes[i] = functionBlock.Genotypes[i].AlleleIndexes[haplotypeIndex];
}
var alleleIndexBlock = new AlleleBlock(functionBlock.PosIndex, alleleIndexes, numRefPosBefore,
numRefPosAfter);
alleleIndexBlocks.Add(alleleIndexBlock);
var currentSampleAlleles = GetSampleAlleles(sampleIndexes, (byte)haplotypeIndex);
UpdateBlockToSampleAlleleMapping(alleleIndexBlock, currentSampleAlleles,
alleleIndexBlockToSampleAllele);
}
for (var i = 0; i < alleleIndexBlocks.Count; i++)
{
for (int j = i + 1; j < alleleIndexBlocks.Count; j++)
{
alleleIndexBlockGraph.AddEdge(alleleIndexBlocks[i], alleleIndexBlocks[j]);
}
}
}
}