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]);
}
}
public void Length_ReturnTrueLength_WhenGapsArePresent()
{
const int expectedResults = 720;
var sequence = new NSequence();
var codingRegion = new CodingRegion(10051, 12770, 51, 800, 720);
const byte startExonPhase = 1;
var regions = new ITranscriptRegion[]
{
new TranscriptRegion(TranscriptRegionType.Exon, 1, 10001, 10299, 1, 299),
new TranscriptRegion(TranscriptRegionType.Intron, 1, 10300, 12300, 229, 331),
new TranscriptRegion(TranscriptRegionType.Exon, 2, 12301, 12970, 331, 1000)
};
var codingSequence = new CodingSequence(sequence, codingRegion, regions, false, startExonPhase);
var observedResults = codingSequence.Length;
Assert.Equal(expectedResults, observedResults);
Assert.NotEqual(expectedResults, codingRegion.End - codingRegion.Start + 1);
}
