CanvasPartition.Segmentation.SegmentGenome C# (CSharp) Method

        public void SegmentGenome(string outPath, SegmentationMethod method, bool isGermline)
        {
            switch (method)
            {
                case SegmentationMethod.Wavelets:
                default:// use Wavelets if CBS is not selected
                    Console.WriteLine("{0} Running Wavelet Partitioning", DateTime.Now);
                    this.Wavelets(isGermline, verbose: 2);
                    break;
                case SegmentationMethod.CBS:
                    Console.WriteLine("{0} Running CBS Partitioning", DateTime.Now);
                    this.CBS(verbose: 2);
                    break;
            }
            Console.WriteLine("{0} Write CanvasPartition results:", DateTime.Now);
            this.WriteCanvasPartitionResults(outPath);
            Console.WriteLine("{0} CanvasPartition results written out", DateTime.Now);
        }

        static int Main(string[] args)
        {
            CanvasCommon.Utilities.LogCommandLine(args);
            string             inFile          = null;
            string             outFile         = null;
            bool               needHelp        = false;
            bool               isGermline      = false;
            string             bedPath         = null;
            double             alpha           = Segmentation.DefaultAlpha;
            SegmentSplitUndo   undoMethod      = SegmentSplitUndo.None;
            SegmentationMethod partitionMethod = SegmentationMethod.Wavelets;
            int       maxInterBinDistInSegment = 1000000;
            OptionSet p = new OptionSet()
            {
                { "i|infile=", "input file - usually generated by CanvasClean", v => inFile = v },
                { "o|outfile=", "text file to output", v => outFile = v },
                { "h|help", "show this message and exit", v => needHelp = v != null },
                { "a|alpha=", "alpha parameter to CBS. Default: " + alpha, v => alpha = float.Parse(v) },
                { "m|method=", "segmentation method (Wavelets/CBS). Default: " + partitionMethod, v => partitionMethod = (SegmentationMethod)Enum.Parse(typeof(SegmentationMethod), v) },
                { "s|split=", "CBS split method (None/Prune/SDUndo). Default: " + undoMethod, v => undoMethod = (SegmentSplitUndo)Enum.Parse(typeof(SegmentSplitUndo), v) },
                { "b|bedfile=", "bed file to exclude (don't span these intervals)", v => bedPath = v },
                { "g|germline", "flag indicating that input file represents germline genome", v => isGermline = v != null },
                { "d|maxInterBinDistInSegment=", "the maximum distance between adjacent bins in a segment (negative numbers turn off splitting segments after segmentation). Default: " + maxInterBinDistInSegment, v => maxInterBinDistInSegment = int.Parse(v) },
            };

            List <string> extraArgs = p.Parse(args);

            if (needHelp)
            {
                ShowHelp(p);
                return(0);
            }

            if (inFile == null || outFile == null)
            {
                ShowHelp(p);
                return(0);
            }

            if (!File.Exists(inFile))
            {
                Console.WriteLine("CanvasPartition.exe: File {0} does not exist! Exiting.", inFile);
                return(1);
            }

            if (!string.IsNullOrEmpty(bedPath) && !File.Exists(bedPath))
            {
                Console.WriteLine("CanvasPartition.exe: File {0} does not exist! Exiting.", bedPath);
                return(1);
            }

            // no command line parameter for segmentation method
            Segmentation SegmentationEngine = new Segmentation(inFile, bedPath, maxInterBinDistInSegment: maxInterBinDistInSegment);

            SegmentationEngine.Alpha      = alpha;
            SegmentationEngine.UndoMethod = undoMethod;
            SegmentationEngine.SegmentGenome(outFile, partitionMethod, isGermline);
            return(0);
        }