public static void CheckSegment(SegmentWithBins segment, int expectedStart, int expectedEnd,
double expectedMedCoverage, int expectedCount)
{
Assert.Equal((uint)expectedStart, segment.Start);
Assert.Equal((uint)expectedEnd, segment.End);
Assert.Equal(expectedMedCoverage, segment.MedianCoverage);
Assert.Equal(expectedCount, segment.Bins.Count);
}
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 Dictionary <string, List <SegmentWithBins> > PostProcessSegments(
GenomeSegmentationResults segmentationResults,
PloidyInfo referencePloidy, Dictionary <string, List <SampleGenomicBin> > excludedIntervals, CoverageInfo coverageInfo)
{
var starts = new Dictionary <string, bool>();
var stops = new Dictionary <string, bool>();
foreach (string chr in segmentationResults.SegmentByChr.Keys)
{
for (int segmentIndex = 0; segmentIndex < segmentationResults.SegmentByChr[chr].Length; segmentIndex++)
{
var segment = segmentationResults.SegmentByChr[chr][segmentIndex];
starts[chr + ":" + segment.start] = true;
stops[chr + ":" + segment.end] = true;
}
}
int segmentNum = -1;
var segmentsByChromosome = new Dictionary <string, List <SegmentWithBins> >();
foreach (string chr in coverageInfo.StartByChr.Keys)
{
segmentsByChromosome.Add(chr, new List <SegmentWithBins>());
SegmentWithBins currentSegment = null;
List <SampleGenomicBin> excludeIntervals = null;
if (excludedIntervals.ContainsKey(chr))
{
excludeIntervals = excludedIntervals[chr];
}
var excludeIndex = 0; // Points to the first interval which *doesn't* end before our current position
uint previousBinEnd = 0;
for (int binIndex = 0; binIndex < coverageInfo.StartByChr[chr].Length; binIndex++)
{
uint start = coverageInfo.StartByChr[chr][binIndex];
uint end = coverageInfo.EndByChr[chr][binIndex];
bool newSegment = IsNewSegment(starts, chr, excludeIntervals, previousBinEnd, end, start, ref excludeIndex, referencePloidy);
var bin = new Bin(start, end, coverageInfo.CoverageByChr[chr][binIndex]);
if (newSegment)
{
segmentNum++;
currentSegment = new SegmentWithBins(segmentNum, bin);
segmentsByChromosome[chr].Add(currentSegment);
}
else
{
if (currentSegment == null)
{
currentSegment = new SegmentWithBins(segmentNum, bin);
segmentsByChromosome[chr].Add(currentSegment);
}
else
{
currentSegment.AddBin(bin);
}
}
previousBinEnd = end;
}
}
return(segmentsByChromosome);
}
