public void GetAltAllelesAndGenotypes_one_sample_ploidy_zero()
{
int[][] alleleCopyNumbers =
{
new[] { -1 }
};
var(altAlleleString, sampleGenotypes) = CanvasSegmentWriter.GetAltAllelesAndGenotypes(alleleCopyNumbers);
string[] expectedGenotypes = { "." };
Assert.Equal(".", altAlleleString);
Assert.Equal(expectedGenotypes, sampleGenotypes);
}
public void GetAltAllelesAndGenotypes_only_reference()
{
int[][] alleleCopyNumbers =
{
new[] { 1, 1 }, // Ref
new[] { 1, 1 } // Ref again
};
var(altAlleleString, sampleGenotypes) = CanvasSegmentWriter.GetAltAllelesAndGenotypes(alleleCopyNumbers);
string[] expectedGenotypes = { "0/0", "0/0" };
Assert.Equal(".", altAlleleString);
Assert.Equal(expectedGenotypes, sampleGenotypes);
}
public void GetAltAllelesAndGenotypes_hemizygous_regions()
{
int[][] alleleCopyNumbers =
{
new[] { 0 }, // Loss
new[] { 1 }, // Ref
new[] { 2 } // Gain
};
var(altAlleleString, sampleGenotypes) = CanvasSegmentWriter.GetAltAllelesAndGenotypes(alleleCopyNumbers);
string[] expectedGenotypes = { "1", "0", "2" };
Assert.Equal("<CN0>,<CN2>", altAlleleString);
Assert.Equal(expectedGenotypes, sampleGenotypes);
}
public void GetAltAllelesAndGenotypes_various_genotypes()
{
int[][] alleleCopyNumbers =
{
new[] { -1, int.MaxValue }, // <DUP>
new[] { 1, 1 }, // Ref
new[] { 0, 1 }, // Loss
new[] { 1, 2 }, // Gain
new[] { 0, 3 }, // Gain
new[] { 2, 2 }, // Gain
new [] { 0, 2 }, // LOH
new [] { -1, -1 }, // CN=2, MCC null
new [] { -1 } // Ploidy == 0
};
var(altAlleleString, sampleGenotypes) = CanvasSegmentWriter.GetAltAllelesAndGenotypes(alleleCopyNumbers);
string[] expectedGenotypes = { "./4", "0/0", "0/1", "0/2", "1/3", "2/2", "1/2", "./.", "." };
Assert.Equal("<CN0>,<CN2>,<CN3>,<DUP>", altAlleleString);
Assert.Equal(expectedGenotypes, sampleGenotypes);
}