public void AddAndGetAlleleCounts()
{
var testRegion = new MyRegionState(1000, 2000);
for (var i = 0; i < 5; i++)
{
testRegion.AddAlleleCount(1001, AlleleType.A, DirectionType.Forward);
}
for (var i = 0; i < 2; i++)
{
testRegion.AddAlleleCount(1001, AlleleType.C, DirectionType.Forward);
}
for (var i = 0; i < 12; i++)
{
testRegion.AddAlleleCount(1001, AlleleType.C, DirectionType.Reverse);
}
for (var i = 0; i < 15; i++)
{
testRegion.AddAlleleCount(2000, AlleleType.A, DirectionType.Stitched);
}
Assert.Equal(testRegion.GetAlleleCount(1001, AlleleType.A, DirectionType.Forward), 5);
Assert.Equal(testRegion.GetAlleleCount(1001, AlleleType.C, DirectionType.Forward), 2);
Assert.Equal(testRegion.GetAlleleCount(1001, AlleleType.C, DirectionType.Reverse), 12);
Assert.Equal(testRegion.GetAlleleCount(2000, AlleleType.A, DirectionType.Stitched), 15);
Assert.Equal(testRegion.GetAlleleCount(1000, AlleleType.A, DirectionType.Stitched), 0);
Assert.Equal(testRegion.GetAlleleCount(1500, AlleleType.A, DirectionType.Forward), 0);
}
public void ExecuteTest_GetCandidates(bool withReference, bool withIntervals)
{
var testRegion = new MyRegionState(1, 50);
var chrReference = new ChrReference()
{
Name = "chr1",
Sequence = string.Concat(Enumerable.Repeat("A", 50))
};
var snv1 = new CandidateAllele("chr1", 5, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new [] { 10, 5, 0 }
};
var snv2 = new CandidateAllele("chr1", 15, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 10, 5, 0 }
};
testRegion.AddCandidate(snv1);
testRegion.AddCandidate(snv2);
for (var i = 0; i < 5; i++)
{
testRegion.AddAlleleCount(5, AlleleType.A, DirectionType.Stitched); // ref @ variant position
testRegion.AddAlleleCount(6, AlleleType.A, DirectionType.Stitched); // ref by itself
testRegion.AddAlleleCount(10, AlleleType.C, DirectionType.Stitched); // nonref by itself (no ref)
testRegion.AddAlleleCount(15, AlleleType.A, DirectionType.Reverse); // ref (multiple directions) + nonref
testRegion.AddAlleleCount(15, AlleleType.A, DirectionType.Forward);
testRegion.AddAlleleCount(15, AlleleType.T, DirectionType.Reverse);
}
ChrIntervalSet intervals = null;
if (withIntervals)
{
intervals = new ChrIntervalSet(new List <Region>()
{
new Region(3, 6),
new Region(16, 16)
}, "chr1");
}
var expectedList = new List <CandidateAllele>();
expectedList.Add(snv1);
expectedList.Add(snv2);
if (withReference)
{
expectedList.Add(new CandidateAllele("chr1", 5, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 5 }
});
expectedList.Add(new CandidateAllele("chr1", 6, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 5 }
});
expectedList.Add(new CandidateAllele("chr1", 10, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 0 }
});
expectedList.Add(new CandidateAllele("chr1", 15, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 5, 5, 0 }
});
}
if (withIntervals)
{
expectedList = expectedList.Where(c => c.Coordinate == 5 || c.Coordinate == 6 || c.Type != AlleleCategory.Reference).ToList();
if (withReference)
{
expectedList.Add(new CandidateAllele("chr1", 3, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 0 }
});
expectedList.Add(new CandidateAllele("chr1", 4, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 0 }
});
expectedList.Add(new CandidateAllele("chr1", 16, "A", "A", AlleleCategory.Reference)
{
SupportByDirection = new[] { 0, 0, 0 }
});
}
}
var allCandidates = testRegion.GetAllCandidates(withReference, chrReference, intervals);
VerifyCandidates(expectedList, allCandidates);
}