public void GetPositionsAndRefAltAlleles_AsExpected()
{
var genotypes = new[] { "1|2", "1/1", "0|1", "0/1" };
var genotypeToSample =
new Dictionary <(string, int), List <int> > {
{ (string.Join(";", genotypes), 0), new List <int> {
0
} }
};
var indexOfUnsupportedVars = Enumerable.Repeat(new HashSet <string>(), genotypes.Length).ToArray();
var starts = new[] { 356, 358, 360, 361 };
var functionBlockRanges = new List <int> {
358, 360, 362, 364
};
var alleles = new[] { new[] { "G", "C", "T" }, new[] { "A", "T" }, new[] { "C", "G" }, new[] { "G", "T" } };
var refSequence = "GAATCG";
var alleleIndexBlocksToSample = AlleleIndexBlock.GetAlleleIndexBlockToSampleIndex(genotypeToSample, indexOfUnsupportedVars, starts, functionBlockRanges).ToArray();
var alleleSet = new AlleleSet(null, starts, alleles);
var alleleIndexBlocks = alleleIndexBlocksToSample.Select(x => x.Key).ToArray();
var decomposedPositionIndex = new HashSet <(int, int)>();
var result1 = VariantGenerator.GetPositionsAndRefAltAlleles(alleleIndexBlocks[0], alleleSet, refSequence, starts[0], decomposedPositionIndex);
var result2 = VariantGenerator.GetPositionsAndRefAltAlleles(alleleIndexBlocks[1], alleleSet, refSequence, starts[0], decomposedPositionIndex);
Assert.Equal((356, 360, "GAATC", "CATTC"), result1);
Assert.Equal((356, 360, "GAATC", "TATTG"), result2);
}
public void GetPositionsAndRefAltAlleles_AsExpected()
{
var genotypeBlock = new GenotypeBlock(new[] { "1|2", "1/1", "0|1", "0/1" }.Select(Genotype.GetGenotype).ToArray());
var genotypeToSample =
new Dictionary <GenotypeBlock, List <int> > {
{ genotypeBlock, new List <int> {
0
} }
};
var indexOfUnsupportedVars = Enumerable.Repeat(new HashSet <int>(), genotypeBlock.Genotypes.Length).ToArray();
var starts = new[] { 356, 358, 360, 361 };
var functionBlockRanges = new List <int> {
358, 360, 362, 364
};
var alleles = new[] { new[] { "G", "C", "T" }, new[] { "A", "T" }, new[] { "C", "G" }, new[] { "G", "T" } };
const string refSequence = "GAATCG";
var alleleBlockToSampleHaplotype = AlleleBlock.GetAlleleBlockToSampleHaplotype(genotypeToSample, indexOfUnsupportedVars, starts, functionBlockRanges, out var alleleBlockGraph);
var mergedAlleleBlockToSampleHaplotype =
AlleleBlockMerger.Merge(alleleBlockToSampleHaplotype, alleleBlockGraph).ToArray();
var alleleSet = new AlleleSet(ChromosomeUtilities.Chr1, starts, alleles);
var alleleBlocks = mergedAlleleBlockToSampleHaplotype.Select(x => x.Key).ToArray();
var sequence = new NSequence();
var result1 = VariantGenerator.GetPositionsAndRefAltAlleles(alleleBlocks[0], alleleSet, refSequence, starts[0], null, sequence, _vidCreator);
var result2 = VariantGenerator.GetPositionsAndRefAltAlleles(alleleBlocks[1], alleleSet, refSequence, starts[0], null, sequence, _vidCreator);
var expectedVarPosIndexes1 = new List <int> {
0, 1
};
var expectedVarPosIndexes2 = new List <int> {
0, 1, 2
};
Assert.Equal((356, 360, "GAATC", "CATTC"), (result1.Start, result1.End, result1.Ref, result1.Alt));
for (var i = 0; i < expectedVarPosIndexes1.Count; i++)
{
Assert.Equal(expectedVarPosIndexes1[i], result1.VarPosIndexesInAlleleBlock[i]);
}
Assert.Equal((356, 360, "GAATC", "TATTG"), (result2.Start, result2.End, result2.Ref, result2.Alt));
for (var i = 0; i < expectedVarPosIndexes2.Count; i++)
{
Assert.Equal(expectedVarPosIndexes2[i], result2.VarPosIndexesInAlleleBlock[i]);
}
}
internal static (int Start, int End, string Ref, string Alt, List <int> VarPosIndexesInAlleleBlock, List <string> decomposedVids) GetPositionsAndRefAltAlleles(AlleleBlock alleleBlock, AlleleSet alleleSet, string totalRefSequence, int regionStart, List <ISimplePosition> simplePositions)
{
int numPositions = alleleBlock.AlleleIndexes.Length;
int firstPositionIndex = alleleBlock.PositionIndex;
int lastPositionIndex = alleleBlock.PositionIndex + numPositions - 1;
int blockStart = alleleSet.Starts[firstPositionIndex];
int blockEnd = alleleSet.Starts[lastPositionIndex];
string lastRefAllele = alleleSet.VariantArrays[lastPositionIndex][0];
int blockRefLength = blockEnd - blockStart + lastRefAllele.Length;
var refSequence = totalRefSequence.Substring(blockStart - regionStart, blockRefLength);
int refSequenceStart = 0;
var altSequenceSegments = new LinkedList <string>();
var variantPosIndexesInAlleleBlock = new List <int>();
var vidListsNeedUpdate = new List <List <string> >();
var decomposedVids = new List <string>();
for (int positionIndex = firstPositionIndex; positionIndex <= lastPositionIndex; positionIndex++)
{
int indexInBlock = positionIndex - firstPositionIndex;
int alleleIndex = alleleBlock.AlleleIndexes[indexInBlock];
//only non-reference alleles considered
if (alleleIndex == 0)
{
continue;
}
variantPosIndexesInAlleleBlock.Add(positionIndex - firstPositionIndex);
string refAllele = alleleSet.VariantArrays[positionIndex][0];
string altAllele = alleleSet.VariantArrays[positionIndex][alleleIndex];
int positionOnRefSequence = alleleSet.Starts[positionIndex] - blockStart;
int refRegionBetweenTwoAltAlleles = positionOnRefSequence - refSequenceStart;
if (refRegionBetweenTwoAltAlleles < 0)
{
string previousAltAllele = alleleSet.VariantArrays[positionIndex - 1][alleleIndex];
throw new UserErrorException($"Conflicting alternative alleles identified at {alleleSet.Chromosome.UcscName}:{alleleSet.Starts[positionIndex]}: both \"{previousAltAllele}\" and \"{altAllele}\" are present.");
}
string refSequenceBefore = refSequence.Substring(refSequenceStart, refRegionBetweenTwoAltAlleles);
altSequenceSegments.AddLast(refSequenceBefore);
altSequenceSegments.AddLast(altAllele);
refSequenceStart = positionOnRefSequence + refAllele.Length;
if (simplePositions == null)
{
continue;
}
var thisPosition = simplePositions[positionIndex];
// alleleIndex is 1-based for altAlleles
int varIndex = alleleIndex - 1;
//Only SNVs get recomposed for now
if (thisPosition.Vids[varIndex] == null)
{
thisPosition.Vids[varIndex] = SmallVariantCreator.GetVid(alleleSet.Chromosome.EnsemblName,
thisPosition.Start, thisPosition.End, thisPosition.AltAlleles[varIndex], VariantType.SNV);
thisPosition.IsDecomposed[varIndex] = true;
}
decomposedVids.Add(thisPosition.Vids[varIndex]);
if (thisPosition.LinkedVids[varIndex] == null)
{
thisPosition.LinkedVids[varIndex] = new List <string>();
}
vidListsNeedUpdate.Add(thisPosition.LinkedVids[varIndex]);
}
altSequenceSegments.AddLast(refSequence.Substring(refSequenceStart));
var recomposedAllele = string.Concat(altSequenceSegments);
var blockRefEnd = blockStart + blockRefLength - 1;
var recomposedVariantId = SmallVariantCreator.GetVid(alleleSet.Chromosome.EnsemblName, blockStart, blockRefEnd, recomposedAllele, VariantType.MNV);
vidListsNeedUpdate.ForEach(x => x.Add(recomposedVariantId));
return(blockStart, blockRefEnd, refSequence, recomposedAllele, variantPosIndexesInAlleleBlock, decomposedVids);
}
decomposedVids) GetPositionsAndRefAltAlleles(AlleleBlock alleleBlock, AlleleSet alleleSet,
string totalRefSequence, int regionStart, List <ISimplePosition> simplePositions, ISequence sequence, IVariantIdCreator vidCreator)
{
int numPositions = alleleBlock.AlleleIndexes.Length;
int firstPositionIndex = alleleBlock.PositionIndex;
int lastPositionIndex = alleleBlock.PositionIndex + numPositions - 1;
int blockStart = alleleSet.Starts[firstPositionIndex];
int blockEnd = alleleSet.Starts[lastPositionIndex];
string lastRefAllele = alleleSet.VariantArrays[lastPositionIndex][0];
int blockRefLength = blockEnd - blockStart + lastRefAllele.Length;
string refSequence = totalRefSequence.Substring(blockStart - regionStart, blockRefLength);
var refSequenceStart = 0;
var altSequenceSegments = new LinkedList <string>();
var variantPosIndexesInAlleleBlock = new List <int>();
var vidListsNeedUpdate = new List <List <string> >();
var decomposedVids = new List <string>();
if (FindConflictAllele(alleleBlock, alleleSet))
{
return(default);
internal static (int Start, int End, string Ref, string Alt) GetPositionsAndRefAltAlleles(AlleleIndexBlock alleleIndexBlock, AlleleSet alleleSet, string totalRefSequence, int regionStart, HashSet <(int, int)> decomposedPosVarIndex)
