NormalizedBinsCoverageCalculator_TwoSegmentsPassingEqualWeighting_ReturnsBedGraphEntriesNormalizedByMedianCopyNumber()
{
var calculator = new NormalizedBinsCoverageCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 4f)
})
{
CopyNumber = 3,
Filter = CanvasFilter.PassFilter
},
new CanvasSegment("chr1", 1, 2, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 1, 2, 8f)
})
{
CopyNumber = 2,
Filter = CanvasFilter.PassFilter
}
};
var results = calculator.Calculate(segments).ToList();
Assert.Equal(2, results.Count);
// normalization factor is average of 3/4 and 2/8 = 0.5
Assert.Equal(2, results[0].Value);
Assert.Equal(4, results[1].Value);
}
NormalizedCoverageCalculator_OneSegmentPassOneSegmentFiltered_ReturnsBedGraphEntriesNormalizedByPassingSegmentCopyNumber()
{
var calculator = new NormalizedBinsCoverageCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 3f)
})
{
CopyNumber = 1,
Filter = CanvasFilter.PassFilter
},
new CanvasSegment("chr1", 1, 2, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 1, 2, 6f)
})
{
CopyNumber = 10,
Filter = CanvasFilter.Create(new[] { "Filtered" })
}
};
var results = calculator.Calculate(segments).ToList();
Assert.Equal(2, results.Count);
Assert.Equal(1, results[0].Value);
Assert.Equal(2, results[1].Value);
}
public void NormalizedBinsCoverageCalculator_NoSegments_ReturnsNoBedGraphEntries()
{
var calculator = new NormalizedBinsCoverageCalculator();
var segments = Enumerable.Empty <CanvasSegment>().ToList();
var results = calculator.Calculate(segments);
Assert.Empty(results);
}
public void NormalizedBinsCoverageCalculator_PrecomputedNormalizationFactor()
{
var calculator = new NormalizedBinsCoverageCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 4f)
})
{
CopyNumber = 3,
Filter = CanvasFilter.PassFilter
},
new CanvasSegment("chr1", 1, 2, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 1, 2, 8f)
})
{
CopyNumber = 2,
Filter = CanvasFilter.PassFilter
}
};
var normalizationFactor = 0.5;
var results = calculator.Calculate(segments, normalizationFactor).ToList();
Assert.Equal(2, results.Count);
Assert.Equal(2, results[0].Value);
Assert.Equal(4, results[1].Value);
normalizationFactor = 1;
results = calculator.Calculate(segments, normalizationFactor).ToList();
Assert.Equal(2, results.Count);
Assert.Equal(4, results[0].Value);
Assert.Equal(8, results[1].Value);
normalizationFactor = 0.25;
results = calculator.Calculate(segments, normalizationFactor).ToList();
Assert.Equal(2, results.Count);
Assert.Equal(1, results[0].Value);
Assert.Equal(2, results[1].Value);
results = calculator.Calculate(new List <CanvasSegment>(), normalizationFactor).ToList();
Assert.Empty(results);
}
public void NormalizedCoverageCalculator_OneSegmentOneBin_ReturnsBedGraphEntryWithSegmentCopyNumber()
{
var calculator = new NormalizedBinsCoverageCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 3f)
})
{
CopyNumber = 2,
Filter = CanvasFilter.PassFilter
}
};
var result = calculator.Calculate(segments).Single();
Assert.Equal(2, result.Value);
}
public void NormalizedBinsCoverageCalculator_SegmentWithNoBins_ReturnsNoBedGraphEntries()
{
var calculator = new NormalizedBinsCoverageCalculator();
var segment = new CanvasSegment("chr1", 100, 120, new List <SampleGenomicBin>());
var segments = new List <CanvasSegment>()
{
segment
};
// Returns no bins because it was given no bins (works if normalization precomputed)
var results = calculator.Calculate(segments, 1);
Assert.Empty(results);
// Throws exception if it tries to compute normalization factor but has nothing to do it with
// If this is a reasonable scenario, might want to make a nicer exception than the unhandled AggregateException
// But I suspect this will never actually happen. For now it's a purely theoretical edge case.
Assert.Throws <AggregateException>(() => calculator.Calculate(segments));
}
NormalizedBinsCoverageCalculator_OneSegmentOneBinCopyNumberZero_ReturnsBedGraphEntryWithZeroCoverage()
{
var calculator = new NormalizedBinsCoverageCalculator();
var segments = new List <CanvasSegment>
{
new CanvasSegment("chr1", 0, 1, new List <SampleGenomicBin>
{
new SampleGenomicBin("chr1", 0, 1, 3f)
})
{
CopyNumber = 0,
Filter = CanvasFilter.PassFilter
}
};
var result = calculator.Calculate(segments).Single();
Assert.Equal("chr1", result.Chromosome);
Assert.Equal(0, result.Interval.Start);
Assert.Equal(1, result.Interval.End);
Assert.Equal(0, result.Value);
}
