public void AddAndGetCandidates_Errors()
{
var testRegion = new MyRegionState(1000, 2000);
Assert.Throws <ArgumentException>(
() => testRegion.AddCandidate(new CandidateAllele("chr1", 999, "A", "T", AlleleCategory.Snv)));
Assert.Throws <ArgumentException>(
() => testRegion.GetAlleleCount(2001, AlleleType.A, DirectionType.Forward));
}
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);
}
public void AddAndGetCandidates()
{
// -----------------------------------------------
// simple test case adding candidate to empty region
// -----------------------------------------------
var testRegion = new MyRegionState(1000, 2000);
var snv1 = new CandidateAllele("chr1", 1500, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 10, 0, 0 }
};
testRegion.AddCandidate(snv1);
var allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 1);
var fetchedCandidate = allCandidates[0];
Assert.True(fetchedCandidate.Equals(snv1));
// -----------------------------------------------
// add same type of candidate but at different position
// -----------------------------------------------
var snv2 = new CandidateAllele("chr1", 1501, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(snv2);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 2);
// make sure coverage is preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 10);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
// -----------------------------------------------
// add a different type of candidate at same position
// -----------------------------------------------
var deletion1 = new CandidateAllele("chr1", 1500, "AT", "A", AlleleCategory.Deletion)
{
SupportByDirection = new[] { 15, 0, 0 }
};
testRegion.AddCandidate(deletion1);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 3);
// make sure coverage is preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 10);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(deletion1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 15);
// -----------------------------------------------
// add same variant, but more coverage
// -----------------------------------------------
var moreSnv1 = new CandidateAllele("chr1", 1500, "A", "T", AlleleCategory.Snv)
{
SupportByDirection = new[] { 2, 0, 0 }, ReadCollapsedCounts = new [] { 9, 8, 7, 6 }
};
testRegion.AddCandidate(moreSnv1);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 3);
// make sure coverage is incremented, read counts incremented
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 12);
for (var i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
Assert.True(fetchedCandidate != null && fetchedCandidate.ReadCollapsedCounts[i] == moreSnv1.ReadCollapsedCounts[i]);
}
// make sure coverage is preserved, read counts preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
for (var i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
Assert.True(fetchedCandidate != null && fetchedCandidate.ReadCollapsedCounts[i] == 0);
}
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(deletion1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 15);
for (var i = 0; i < Constants.NumReadCollapsedTypes; i++)
{
Assert.True(fetchedCandidate != null && fetchedCandidate.ReadCollapsedCounts[i] == 0);
}
var moreDeletion1 = new CandidateAllele("chr1", 1500, "AT", "A", AlleleCategory.Deletion)
{
SupportByDirection = new[] { 0, 18, 0 }
};
testRegion.AddCandidate(moreDeletion1);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 3);
// make sure coverage is incremented
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(deletion1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 33);
// make sure coverage is preserved
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv1));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 12);
fetchedCandidate = allCandidates.FirstOrDefault(c => c.Equals(snv2));
Assert.True(fetchedCandidate != null && fetchedCandidate.Support == 5);
// -----------------------------------------------
// add insertion that goes off block
// -----------------------------------------------
var edgeInsertion = new CandidateAllele("chr1", 2000, "A", "TCG", AlleleCategory.Insertion)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeInsertion);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 4);
Assert.Equal(2001, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add mnv that goes off block
// -----------------------------------------------
var edgeMnv = new CandidateAllele("chr1", 1999, "ATCC", "TCGG", AlleleCategory.Mnv)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeMnv);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 5);
Assert.Equal(2002, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add deletion that goes off block
// -----------------------------------------------
var edgeDeletion = new CandidateAllele("chr1", 1999, "A" + new string('T', 25), "A", AlleleCategory.Deletion)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeDeletion);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 6);
Assert.Equal(2025, testRegion.MaxAlleleEndpoint);
// -----------------------------------------------
// add variant that goes off block but not as far as the deletion did - max endpoint should stay the same
// -----------------------------------------------
var edgeMnv2 = new CandidateAllele("chr1", 1999, "ATCGA", "TCGCT", AlleleCategory.Mnv)
{
SupportByDirection = new[] { 5, 0, 0 }
};
testRegion.AddCandidate(edgeMnv2);
allCandidates = testRegion.GetAllCandidates(false, null);
Assert.Equal(allCandidates.Count, 7);
Assert.Equal(2025, testRegion.MaxAlleleEndpoint);
}