CanvasBin.FragmentBinner.Bin C# (CSharp) Method

        public int Bin()
        {
            if (parameters.predefinedBinsFile == null)
            {
                throw new ApplicationException("Predefined bins in BED is required for fragment binning.");
            }
            if (!parameters.isPairedEnd) // Janus-SRS-189
            {
                throw new ApplicationException("Paired-end reads are required for fragment binning.");
            }

            Dictionary<string, List<GenomicBin>> predefinedBins = Utilities.LoadBedFile(parameters.predefinedBinsFile, gcIndex: 3);
            List<string> chromosomes = GetChromosomesInBam(); // used to order chromosomes

            if (!Utilities.IsSubset(predefinedBins.Keys, chromosomes))
            {
                throw new ApplicationException(
                    String.Format("Not all chromosomes in {0} are found in {1}.", parameters.predefinedBinsFile, parameters.bamFile));
            }

            // Count fragments by chromosome
            List<ThreadStart> binningThreads = new List<ThreadStart>();
            List<BinTask> tasks = new List<BinTask>();
            foreach (string chrom in chromosomes)
            {
                if (!predefinedBins.ContainsKey(chrom)) { continue; }
                BinTask task = new BinTask(parameters.referenceFile, chrom, parameters.bamFile, predefinedBins[chrom]);
                tasks.Add(task);
                binningThreads.Add(new ThreadStart(() => { task.DoIt(); }));
            }

            Console.WriteLine("Launch fragment binning jobs...");
            Console.Out.WriteLine();
            Parallel.ForEach(binningThreads, t => { t.Invoke(); });
            Console.WriteLine("Completed fragment binning jobs.");
            Console.Out.WriteLine();

            long usableFragmentCount = tasks.Select(t => t.UsableFragmentCount).Sum();
            if (usableFragmentCount == 0)
            {
                throw new ApplicationException(String.Format("No passing-filter fragments overlapping bins are found in {0}", parameters.bamFile));
            }

            // Aggregate bins
            List<GenomicBin> finalBins = new List<GenomicBin>();
            foreach (string chrom in chromosomes)
            {
                if (!predefinedBins.ContainsKey(chrom)) { continue; }
                finalBins.AddRange(predefinedBins[chrom]);
            }

            // Output!
            CanvasIO.WriteToTextFile(parameters.outFile, finalBins);

            return 0;
        }

        public void TestAllChromsInBedAreInBam()
        {
            CanvasBinParameters parameters = new CanvasBinParameters();
            string assemblyFolder = Isas.Shared.Utilities.GetAssemblyFolder(typeof(TestCanvasBin));
            string dataFolder = Path.Combine(assemblyFolder, "Data");
            parameters.predefinedBinsFile = Path.Combine(dataFolder, "bins_chrU.bed");
            parameters.bamFile = Path.Combine(dataFolder, "single-end.bam");
            parameters.isPairedEnd = true;

            FragmentBinner fragmentBinner = new FragmentBinner(parameters);
            bool exceptionCaught = false;
            try
            {
                fragmentBinner.Bin();
            }
            catch (ApplicationException e)
            {
                if (e.Message.Contains(String.Format("Not all chromosomes in {0} are found in {1}.", parameters.predefinedBinsFile, parameters.bamFile)))
                    exceptionCaught = true;
            }
            Assert.IsTrue(exceptionCaught);
        }