/// <summary>
/// Remap GenomicBin from genome coordiantes into CanvasBin coordiantes
/// </summary>
public static List <SampleGenomicBin> RemapCommonRegions(List <SampleGenomicBin> commonRegions, uint[] startByChr, uint[] endByChr)
{
var length = startByChr.Length;
var index = 0;
List <SampleGenomicBin> commonRegionsRemapped = new List <SampleGenomicBin>();
foreach (SampleGenomicBin commonRegion in commonRegions)
{
if (index > length)
{
break;
}
var startSegment = RemapIndex(startByChr, endByChr, commonRegion.Start, length, ref index);
var endSegment = RemapIndex(startByChr, endByChr, commonRegion.Stop, length, ref index);
if (startSegment.HasValue && endSegment.HasValue)
{
SampleGenomicBin interval = new SampleGenomicBin();
interval.Start = startSegment.Value;
interval.Stop = endSegment.Value;
commonRegionsRemapped.Add(interval);
}
}
return(commonRegionsRemapped);
}
public void TestBins()
{
SampleGenomicBin bin = new SampleGenomicBin("chr1", 12345, 678910, 20, 100);
Assert.Equal(666565, bin.Size);
}
private static BedGraphEntry GetBedGraphEntry(SampleGenomicBin bin, double normalizationFactor)
{
var normalizedCoverage = (decimal)(bin.Count * normalizationFactor);
return(new BedGraphEntry(bin.GenomicBin.Chromosome, bin.GenomicBin.Interval, normalizedCoverage));
}
