public void Run(ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager) { CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, true, CanvasCoverageMode.GCContentWeighted, 100, CommonOptions.CustomParams); var callset = GetCallset(); runner.CallSample(callset); }
public void Run(ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager) { CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, false, CanvasCoverageMode.TruncatedDynamicRange, 100, CommonOptions.CustomParams); var callset = GetCallset(); logger.Info($"Normal Vcf path: {callset.NormalVcfPath}"); runner.CallSample(callset); }
public void Run(ILogger logger, ICheckpointRunnerAsync checkpointRunner, IWorkManager workManager) { CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, true, CanvasCoverageMode.TruncatedDynamicRange, 300, CommonOptions.CustomParams); var callset = GetCallset(logger); runner.CallSample(callset); }
public CanvasRunner(ILogger logger, IWorkManager workManager, ICheckpointRunnerAsync checkpointRunner, bool isSomatic, CanvasCoverageMode coverageMode, int countsPerBin, Dictionary<string, string> customParameters = null) { _logger = logger; _workManager = workManager; _checkpointRunner = checkpointRunner; _isSomatic = isSomatic; _canvasFolder = Path.Combine(Utilities.GetAssemblyFolder(typeof(CanvasRunner))); _coverageMode = coverageMode; _countsPerBin = countsPerBin; if (customParameters != null) { _customParameters = new Dictionary<string, string>(customParameters, StringComparer.InvariantCultureIgnoreCase); } }
public CanvasRunner(ILogger logger, IWorkManager workManager, ICheckpointRunnerAsync checkpointRunner, bool isSomatic, CanvasCoverageMode coverageMode, int countsPerBin, Dictionary <string, string> customParameters = null) { _logger = logger; _workManager = workManager; _checkpointRunner = checkpointRunner; _isSomatic = isSomatic; _canvasFolder = Path.Combine(Utilities.GetAssemblyFolder(typeof(CanvasRunner))); _coverageMode = coverageMode; _countsPerBin = countsPerBin; if (customParameters != null) { _customParameters = new Dictionary <string, string>(customParameters, StringComparer.InvariantCultureIgnoreCase); } }