public void AddBinTest()
{
var bin1 = new Bin(100, 2000, 10d);
var bin2 = new Bin(2500, 3000, 5d);
var bin3 = new Bin(5000, 8000, 45d);
var segmentWithBins = new SegmentWithBins(1, bin1);
SegmentTestHelpers.CheckSegment(segmentWithBins, 100, 2000, 10, 1);
segmentWithBins.AddBin(bin2);
SegmentTestHelpers.CheckSegment(segmentWithBins, 100, 3000, 7.5, 2);
segmentWithBins.AddBin(bin3);
SegmentTestHelpers.CheckSegment(segmentWithBins, 100, 8000, 10, 3);
// Order they are added in should not affect final result
segmentWithBins = new SegmentWithBins(1, bin1);
segmentWithBins.AddBin(bin3);
segmentWithBins.AddBin(bin2);
SegmentTestHelpers.CheckSegment(segmentWithBins, 100, 8000, 10, 3);
}
public void PostProcessSegmentsTests()
{
var processor = new SegmentationResultsProcessor(100);
var chr1Segments = new List <SegmentationInput.Segment>();
chr1Segments.Add(new SegmentationInput.Segment()
{
start = 1, end = 1000
});
chr1Segments.Add(new SegmentationInput.Segment()
{
start = 1100, end = 4500
});
chr1Segments.Add(new SegmentationInput.Segment()
{
start = 4600, end = 5000
});
var segmentsByChrom = new Dictionary <string, SegmentationInput.Segment[]>();
segmentsByChrom.Add("chr1", chr1Segments.ToArray());
var segmentationResults = new GenomeSegmentationResults(segmentsByChrom);
var ploidyInfo = new PloidyInfo();
var excludedIntervals = new Dictionary <string, List <SampleGenomicBin> >();
var coverageInfo = new CoverageInfo();
coverageInfo.CoverageByChr = new Dictionary <string, double[]>();
coverageInfo.EndByChr = new Dictionary <string, uint[]>();
coverageInfo.StartByChr = new Dictionary <string, uint[]>();
coverageInfo.CoverageByChr.Add("chr1", new double[] { 10, 10, 50, 100, 25, 10 });
coverageInfo.StartByChr.Add("chr1", new uint[] { 100, 600, 1200, 1300, 4001, 5000 });
coverageInfo.EndByChr.Add("chr1", new uint[] { 500, 890, 1299, 4000, 4500, 5050 });
var results = processor.PostProcessSegments(segmentationResults, ploidyInfo, excludedIntervals, coverageInfo);
var chr1Results = results["chr1"];
Assert.Equal(3, chr1Results.Count);
// Final segments should reflect boundaries of actual bins within them
// (in practice, these probably shouldn't disagree? but let's go theoretical here)
SegmentTestHelpers.CheckSegment(chr1Results[0], 100, 890, 10, 2);
SegmentTestHelpers.CheckSegment(chr1Results[1], 1200, 4500, 50, 3);
SegmentTestHelpers.CheckSegment(chr1Results[2], 5000, 5050, 10, 1); // Bin extends past segment - still keep it (?)
// Add forbidden zone between two bins of the same original segment, this should split up the affected segment
excludedIntervals.Add("chr1", new List <SampleGenomicBin>()
{
GetForbiddenZone("chr1", 525, 575)
}); // Mid = 550, in between the bins of the first segment
results = processor.PostProcessSegments(segmentationResults, ploidyInfo, excludedIntervals, coverageInfo);
chr1Results = results["chr1"];
Assert.Equal(4, chr1Results.Count);
SegmentTestHelpers.CheckSegment(chr1Results[0], 100, 500, 10, 1);
SegmentTestHelpers.CheckSegment(chr1Results[1], 600, 890, 10, 1);
SegmentTestHelpers.CheckSegment(chr1Results[2], 1200, 4500, 50, 3);
SegmentTestHelpers.CheckSegment(chr1Results[3], 5000, 5050, 10, 1); // Bin extends past segment - still keep it (?)
// Forbidden zone midpoint is in the second bin -- apparently this is presumed to never happen because it would have already been taken care of
// This fails the test with the Debug Asserts in there. Otherwise it would be counted as a new bin
excludedIntervals.Clear();
excludedIntervals.Add("chr1", new List <SampleGenomicBin>()
{
GetForbiddenZone("chr1", 585, 635)
}); // Mid = 610, in second bin
results = processor.PostProcessSegments(segmentationResults, ploidyInfo, excludedIntervals, coverageInfo);
chr1Results = results["chr1"];
Assert.Equal(4, chr1Results.Count);
SegmentTestHelpers.CheckSegment(chr1Results[0], 100, 500, 10, 1);
SegmentTestHelpers.CheckSegment(chr1Results[1], 600, 890, 10, 1);
SegmentTestHelpers.CheckSegment(chr1Results[2], 1200, 4500, 50, 3);
SegmentTestHelpers.CheckSegment(chr1Results[3], 5000, 5050, 10, 1); // Bin extends past segment - still keep it (?)
// Forbidden zone midpoint is in the first bin although it ends between bins -- apparently this is presumed to never happen because it would have already been taken care of
// Note the asymmetry compared to the above
excludedIntervals.Clear();
excludedIntervals.Add("chr1", new List <SampleGenomicBin>()
{
GetForbiddenZone("chr1", 465, 515)
}); // Mid = 490, in first bin of first segment
results = processor.PostProcessSegments(segmentationResults, ploidyInfo, excludedIntervals, coverageInfo);
chr1Results = results["chr1"];
// Would fail - asymmetry. What do we want?
// Leave as-is for now so as not to change the behavior in this (unrelated) feature addition
//Assert.Equal(4, chr1Results.Count);
//SegmentTestHelpers.CheckSegment(chr1Results[0], 100, 500, 10, 1);
//SegmentTestHelpers.CheckSegment(chr1Results[1], 600, 890, 10, 1);
//SegmentTestHelpers.CheckSegment(chr1Results[2], 1200, 4500, 50, 3);
//SegmentTestHelpers.CheckSegment(chr1Results[3], 5000, 5050, 10, 1); // Bin extends past segment - still keep it (?)
// TODO test where no segment covers bins?
// TODO overlapping segments or bins?
// TODO bin starts before segment
// TODO test interbin dist
}
