private static List <OverlappingSegmentsRegion> GetSegmentSets(int defaultAlleleCountThreshold, Dictionary <string, List <BedEntry> > commonRegions,
Dictionary <string, IReadOnlyList <SampleGenomicBin> > genomicBinsByChromosome, Dictionary <string, List <BedInterval> > segmentIntervalsByChromosome,
Dictionary <string, List <Balleles> > allelesByChromosomeCommonSegs, Segments segments)
{
var segmentsSetByChromosome = new ConcurrentDictionary <string, List <OverlappingSegmentsRegion> >();
Parallel.ForEach(
segments.GetChromosomes(),
chr =>
{
var segmentsByChromosome = segments.GetSegmentsForChromosome(chr).ToList();
if (commonRegions.Keys.Any(chromosome => chromosome == chr))
{
var commonCnvCanvasSegments = CanvasSegment.CreateSegmentsFromCommonCnvs(genomicBinsByChromosome[chr],
segmentIntervalsByChromosome[chr], allelesByChromosomeCommonSegs[chr]);
segmentsSetByChromosome[chr] = CanvasSegment.MergeCommonCnvSegments(segmentsByChromosome,
commonCnvCanvasSegments, defaultAlleleCountThreshold);
}
else
{
segmentsSetByChromosome[chr] = segmentsByChromosome.Select(
segment => new OverlappingSegmentsRegion(new List <CanvasSegment> {
segment
}, null)).ToList();
}
});
return(segmentsSetByChromosome.OrderBy(i => i.Key).Select(x => x.Value).SelectMany(x => x).ToList());
}
