public void TrimTaillingRefAlleles_RefIsTrimmed()
{
var blocks = new[]
{
new List <int> {
1, 2, 1, 0, 1, 0, 0
},
new List <int> {
0, 2, 1, 0, 1, 1, 0
}
};
var expected = new[]
{
new List <int> {
1, 2, 1, 0, 1, 0
},
new List <int> {
0, 2, 1, 0, 1, 1
}
};
AlleleIndexBlock.TrimTrailingRefAlleles(blocks);
Assert.Equal(expected, blocks);
}
public void GetPloidyFromGenotypes_DotIsIgnored()
{
string genotypes = ".;1|2;0/2";
var ploidy = AlleleIndexBlock.GetMaxPloidy(genotypes);
Assert.Equal(2, ploidy);
}
private static VariantInfo GetVariantInfo(PositionSet positionSet, AlleleIndexBlock alleleIndexBlock)
{
string filter = "PASS";
var positions = positionSet.SimplePositions;
var startIndex = alleleIndexBlock.PositionIndex;
var numPositions = alleleIndexBlock.AlleleIndexes.Count;
var numSamples = positionSet.NumSamples;
string[] quals = new string[numPositions];
for (int i = startIndex; i < startIndex + numPositions; i++)
{
quals[i - startIndex] = positions[i].VcfFields[VcfCommon.QualIndex];
string thisFilter = positions[i].VcfFields[VcfCommon.FilterIndex];
if (filter == "PASS" && thisFilter != "PASS" && thisFilter != ".")
{
filter = FailedFilterTag;
}
}
string qual = GetStringWithMinValueOrDot(quals);
string[] gqValues = new string[numSamples];
for (int i = 0; i < numSamples; i++)
{
gqValues[i] = GetStringWithMinValueOrDot(new ArraySegment <string>(positionSet.GqInfo[i], startIndex, numPositions).ToArray());
}
string[] psValues = new string[numSamples];
for (int i = 0; i < numSamples; i++)
{
// PS tags are the same in the decomposed variants
psValues[i] = positionSet.PsInfo[i][startIndex];
}
return(new VariantInfo(qual, filter, gqValues, psValues));
}
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);
}
internal static (int Start, int End, string Ref, string Alt) GetPositionsAndRefAltAlleles(AlleleIndexBlock alleleIndexBlock, AlleleSet alleleSet, string totalRefSequence, int regionStart, HashSet <(int, int)> decomposedPosVarIndex)