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;
}
