public void Run(ILogger logger, ICheckpointRunner checkpointRunner, IWorkManager workManager, IFileLocation runtimeExecutable) { CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, runtimeExecutable, 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, true, CanvasCoverageMode.GCContentWeighted, 300, CommonOptions.CustomParams); var callset = GetCallset(logger); runner.CallSample(callset); }
public void Run(ILogger logger, ICheckpointRunner checkpointRunner, IWorkManager workManager, IFileLocation runtimeExecutable) { CanvasRunner runner = new CanvasRunner(logger, workManager, checkpointRunner, runtimeExecutable, false, CanvasCoverageMode.TruncatedDynamicRange, 100, CommonOptions.CustomParams); var callset = GetCallset(); var spwWorkflow = new SmallPedigreeWorkflow(runner); spwWorkflow.CallPedigree(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 GetExecutablePath_test() { var logger = Substitute.For <ILogger>(); var workDoer = Substitute.For <IWorkDoer>(); var checkpointRunner = Substitute.For <ICheckpointRunner>(); Func <string, ICommandFactory> runtimePrefix = component => Substitute.For <ICommandFactory>(); string dotnetPath = @"C:\path\to\dotnet.exe"; var runtimeExecutable = new FileLocation(dotnetPath); bool isSomatic = true; var coverageMode = new CanvasCoverageMode(); int countsPerBin = 0; string canvasFolder = @"C:\path\to\Canvas\"; var bAlleleBedGraphWriter = Substitute.For <IBAlleleBedGraphWriter>(); var canvasRunner = new CanvasRunner(logger, workDoer, checkpointRunner, runtimeExecutable, runtimePrefix, isSomatic, coverageMode, countsPerBin, bAlleleBedGraphWriter, null, canvasFolder); string prefix = "something before "; var commandLineBuilder = new StringBuilder(prefix); string canvasExecutableStub = "CanvasBin"; string fullName = canvasRunner.GetExecutablePath(canvasExecutableStub, commandLineBuilder); Assert.Equal(@"C:\path\to\dotnet.exe", fullName); Assert.Equal(@"something before C:\path\to\Canvas\CanvasBin\CanvasBin.dll ", commandLineBuilder.ToString()); }
public SmallPedigreeWorkflow(CanvasRunner runner) { _runner = runner; }