public void AddAndGetAlleleCounts()
{
var testRegion = new RegionState(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);
}
private IAlleleSource CreateMockStateManager(List <AlleleCount> states, int refCounts = 0)
{
var mockAlleleCountSource = new Mock <IAlleleSource>();
var numAnchorTypes = 5;
var regionState = new RegionState(1, 1000, numAnchorTypes);
foreach (var state in states)
{
for (var directionIndex = 0; directionIndex < Constants.NumDirectionTypes; directionIndex++)
{
for (var anchorIndex = 0; anchorIndex < numAnchorTypes * 2 + 1; anchorIndex++)
{
for (var i = 0; i < state.DirectionCoverage[directionIndex, anchorIndex]; i++)
{
regionState.AddAlleleCount(state.Coordinate, state.AlleleType, (DirectionType)directionIndex, anchorIndex);
}
}
}
mockAlleleCountSource.Setup(
s => s.GetAlleleCount(state.Coordinate,
state.AlleleType,
It.IsAny <DirectionType>(), It.IsAny <int>(), It.IsAny <int?>(), It.IsAny <bool>(), It.IsAny <bool>()))
.Returns((int c, AlleleType a, DirectionType d, int minAnchor, int?maxAnchor, bool fromEnd, bool symm) =>
{
return(regionState.GetAlleleCount(c, a, d, minAnchor, maxAnchor, fromEnd, symm));
}
);
}
mockAlleleCountSource.Setup(c => c.GetGappedMnvRefCount(It.IsAny <int>())).Returns(refCounts);
return(mockAlleleCountSource.Object);
}
public void ExecuteTest_GetCandidates(bool withReference, bool withIntervals)
{
var testRegion = new RegionState(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 <CallSomaticVariants.Logic.RegionState.Region>()
{
new CallSomaticVariants.Logic.RegionState.Region(3, 6),
new CallSomaticVariants.Logic.RegionState.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);
}
