Пример #1
0
        private void Initialize()
        {
            var baseReader = new BamReader(_inputBam);

            _chroms     = baseReader.GetReferenceNames();
            _header     = baseReader.GetHeader();
            _references = baseReader.GetReferences();
            _header     = BamStitcher.UpdateBamHeader(_header);
        }
Пример #2
0
        public void Process(string inputBam, string outFolder, StitcherOptions stitcherOptions)
        {
            var jobManager   = new JobManager(10);
            var jobs         = new List <IJob>();
            var perChromBams = new List <string>();

            // Process each of the chromosomes separately
            foreach (var chrom in _chroms)
            {
                var intermediateOutput = Path.Combine(outFolder, Path.GetFileNameWithoutExtension(inputBam) + "." + chrom + ".stitched.bam");
                perChromBams.Add(intermediateOutput);
                var stitcher = new BamStitcher(inputBam, intermediateOutput, stitcherOptions, chrFilter: chrom);
                jobs.Add(new GenericJob(() => stitcher.Execute(), "Stitcher_" + chrom));
            }

            jobManager.Process(jobs);

            // Combine the per-chromosome bams
            Logger.WriteToLog("Writing final bam.");

            var outputBam = Path.Combine(outFolder, Path.GetFileNameWithoutExtension(inputBam) + ".final.stitched.bam");

            using (var finalOutput = new BamWriter(outputBam, _header, _references))
            {
                foreach (var bam in perChromBams)
                {
                    Logger.WriteToLog("Adding " + bam + " to final bam.");
                    var bamAlignment = new BamAlignment();

                    using (var bamReader = new BamReader(bam))
                    {
                        while (true)
                        {
                            var hasMoreReads = bamReader.GetNextAlignment(ref bamAlignment, false);
                            if (!hasMoreReads)
                            {
                                break;
                            }
                            finalOutput.WriteAlignment(bamAlignment);
                        }
                    }

                    File.Delete(bam);
                }
            }

            Logger.WriteToLog("Finished combining per-chromosome bams into final bam at " + outputBam);
        }
Пример #3
0
        public void Process(string inputBam, string outFolder, StitcherOptions stitcherOptions)
        {
            var stitcher = new BamStitcher(inputBam, Path.Combine(outFolder, Path.GetFileNameWithoutExtension(inputBam) + ".stitched.bam"), stitcherOptions);

            stitcher.Execute();
        }