CanvasClean.CanvasClean.NormalizeByGC C# (CSharp) Method

        static void NormalizeByGC(List<GenomicBin> bins, NexteraManifest manifest = null)
        {
            // DebugPrintCountsByGC(bins, "CountsByGC-Before.txt");
            // An array of lists. Each array element (0-100) will hold a list of counts whose bins have the same GC content.
            List<float>[] countsByGC;

            // Will hold all of the autosomal counts present in 'bins'
            List<float> counts;
            EnrichmentUtilities.GetCountsByGC(bins, manifest, out countsByGC, out counts);

            double globalMedian = Utilities.Median(counts);
            double?[] medians = new double?[countsByGC.Length];

            // Compute the median count for each GC bin
            for (int gcBinIndex = 0; gcBinIndex < countsByGC.Length; gcBinIndex++)
            {
                if (countsByGC[gcBinIndex].Count >= defaultMinNumberOfBinsPerGC)
                {
                    medians[gcBinIndex] = Utilities.Median(countsByGC[gcBinIndex]);
                }
                else
                {
                    List<Tuple<float, float>> weightedCounts = GetWeightedCounts(countsByGC, gcBinIndex);
                    medians[gcBinIndex] = Utilities.WeightedMedian(weightedCounts);
                }
            }

            // Divide each count by the median count of bins with the same GC content
            for (int gcBinIndex = 0; gcBinIndex < bins.Count; gcBinIndex++)
            {
                double? median = medians[bins[gcBinIndex].GC];
                if (median != null && median > 0)
                    bins[gcBinIndex].Count = (float)(globalMedian * (double)bins[gcBinIndex].Count / median);
            }
            // DebugPrintCountsByGC(bins, "CountsByGC-After.txt");
        }