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 AddAndGetCandidates_Errors()
{
var testRegion = new RegionState(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 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);
}
