public void NormalizedSegmentsCoverageCalculator_NoBins_ReturnsNoBedGraphEntries()
{
var calculator = new NormalizedSegmentsCoverageCalculator();
var segments = Enumerable.Empty <CanvasSegment>().ToList();
var results = calculator.Calculate(segments);
Assert.Empty(results);
}
public void NormalizedSegmentsCoverageCalculator_TestMedianCoverages()
{
var calculator = new NormalizedSegmentsCoverageCalculator();
var segments = new List <CanvasSegment>();
// Median of 10 = 10
var segment1 = GetSegment("chr1", 20, 30);
AddBin(segment1, "chr1", 20, 30, 10);
segments.Add(segment1);
// Median of 20,30,50 = 30
var segment2 = GetSegment("chr1", 40, 70);
AddBin(segment2, "chr1", 40, 50, 20);
AddBin(segment2, "chr1", 51, 60, 30);
AddBin(segment2, "chr1", 61, 70, 50);
segments.Add(segment2);
// Median of 60,80 = 70
var segment3 = GetSegment("chr2", 20, 50);
AddBin(segment3, "chr2", 20, 30, 60);
AddBin(segment3, "chr2", 40, 50, 80);
segments.Add(segment3);
var segment4 = GetSegment("chr3", 20, 50);
AddBin(segment4, "chr3", 20, 30, 0);
AddBin(segment4, "chr3", 40, 50, 0);
segments.Add(segment4);
var entries = calculator.Calculate(segments, 1).ToList();
Assert.Equal(4, entries.Count());
CheckBedEntry(entries[0], 20, 30, "chr1", 10);
CheckBedEntry(entries[1], 40, 70, "chr1", 30);
CheckBedEntry(entries[2], 20, 50, "chr2", 70);
CheckBedEntry(entries[3], 20, 50, "chr3", 0);
entries = calculator.Calculate(segments, 0.5).ToList();
Assert.Equal(4, entries.Count());
CheckBedEntry(entries[0], 20, 30, "chr1", 5);
CheckBedEntry(entries[1], 40, 70, "chr1", 15);
CheckBedEntry(entries[2], 20, 50, "chr2", 35);
CheckBedEntry(entries[3], 20, 50, "chr3", 0);
}
public void NormalizedSegmentsCoverageCalculator_OneSegmentOneBinCopyNumberZero_ReturnsBedGraphEntryWithZeroCoverage()
{
var calculator = new NormalizedSegmentsCoverageCalculator();
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);
}
