public IParsingResult <IModeLauncher> Parse(
MainParser main, ILogger logger, ISettings settings, ICheckpointRunner checkpointRunner,
IWorkDoer workDoer, string[] args, TextWriter standardWriter, TextWriter errorWriter)
{
var results = main.GetParseResults(args);
var parsingResult = checkpointRunner.RunCheckpoint("Validate input", () =>
{
if (!results.Validate(out IParsingResult <IModeLauncher> failedResult))
{
return(ParsingResult <T> .FailedResult(failedResult.ErrorMessage));
}
var successfulResults = new SuccessfulResultCollection(results);
var commonOptions = successfulResults.Get(MainParser.CommonOptionsParser);
return(GetSerializedResult(successfulResults, commonOptions));
});
if (!parsingResult.Success)
{
ShowError(main, logger.Error, parsingResult.ErrorMessage);
return(ParsingResult <IModeLauncher> .FailedResult(parsingResult));
}
var runner = GetRunner(parsingResult.Result);
return(ParsingResult <IModeLauncher> .SuccessfulResult(new ModeLauncher(logger, settings, checkpointRunner, workDoer, runner, args, main.GetVersion(), Name)));
}
public CoverageVisualizationWriterFactory(ILogger logger, IWorkDoer workDoer, ICommandManager commandManager, GenomeMetadata genome)
{
_logger = logger;
_workDoer = workDoer;
_commandManager = commandManager;
_genome = genome;
}
private IParsingResult <IModeLauncher> Parse(
ILogger logger, ISettings settings, ICheckpointRunner checkpointRunner,
IWorkDoer workDoer, string[] args, TextWriter standardWriter, TextWriter errorWriter)
{
var mode = _modeParsers[args[0]];
return(mode.Parse(this, logger, settings, checkpointRunner, workDoer, args, standardWriter, errorWriter));
}
public CanvasRunnerFactory(ILogger logger, ICheckpointRunner checkpointRunner,
IWorkDoer workDoer, IFileLocation runtimeExecutable, Func <string, ICommandFactory> runtimeCommandPrefix)
{
_logger = logger;
_checkpointRunner = checkpointRunner;
_workDoer = workDoer;
_runtimeExecutable = runtimeExecutable;
_runtimeCommandPrefix = runtimeCommandPrefix;
}
public ChunkReaderQueue(IChunkReader chunkReader, IWorkDoer workDoer, int queueLength)
{
_WorkDoer = workDoer;
_QueueLength = queueLength;
ChunkReader = chunkReader;
_WaitForAddEvent = new ManualResetEventSlim(false);
_WaitForRemoveEvent = new ManualResetEventSlim(true);
_ChunkInProgressIndices = new int[workDoer.ThreadCount];
}
public SmallPedigreeCheckpointFactory(
IWorkDoer workDoer,
ILogger logger,
ExecutableProcessor executableProcessor,
IFileLocation pedigreefileNameStub,
CanvasWorkerFactory canvasWorkerFactory)
{
_workDoer = workDoer;
_logger = logger;
_executableProcessor = executableProcessor;
_pedigreefileNameStub = pedigreefileNameStub;
_canvasWorkerFactory = canvasWorkerFactory;
}
public ModeLauncher(
ILogger logger, ISettings settings, ICheckpointRunner checkpointRunner,
IWorkDoer workDoer, IModeRunner modeRunner, IEnumerable <string> args, string version, string mode)
{
_logger = logger;
_settings = settings;
_checkpointRunner = checkpointRunner;
_workDoer = workDoer;
_modeRunner = modeRunner;
_args = args;
_version = version;
_mode = mode;
}
public CanvasEnrichmentCnvCaller(IWorkDoer workDoer, ILogger logger, IFileLocation canvasExe, IFileLocation runtimeExecutable,
ICanvasAnnotationFileProvider annotationFileProvider,
ICanvasSingleSampleInputCommandLineBuilder singleSampleInputCommandLineBuilder,
CanvasEnrichmentInputCreator <CanvasEnrichmentInput> enrichmentInputCreator,
CanvasPloidyVcfCreator canvasPloidyVcfCreator)
{
_workDoer = workDoer;
_logger = logger;
_canvasExe = canvasExe;
_runtimeExecutable = runtimeExecutable;
_annotationFileProvider = annotationFileProvider;
_singleSampleInputCommandLineBuilder = singleSampleInputCommandLineBuilder;
_enrichmentInputCreator = enrichmentInputCreator;
_canvasPloidyVcfCreator = canvasPloidyVcfCreator;
}
public CanvasSmallPedigreeWrapper(
IWorkDoer workDoer,
ILogger logger,
IFileLocation canvasExe, IFileLocation runtimeExecutable,
ICanvasAnnotationFileProvider annotationFileProvider,
ICanvasSingleSampleInputCommandLineBuilder singleSampleInputCommandLineBuilder,
CanvasPloidyVcfCreator canvasPloidyVcfCreator)
{
_workDoer = workDoer;
_logger = logger;
_canvasExe = canvasExe;
_annotationFileProvider = annotationFileProvider;
_singleSampleInputCommandLineBuilder = singleSampleInputCommandLineBuilder;
_canvasPloidyVcfCreator = canvasPloidyVcfCreator;
_runtimeExecutable = runtimeExecutable;
}
public CanvasWorkerFactory(
ISettings sampleSettings,
IWorkDoer workDoer,
ILogger logger,
ExecutableProcessor executableProcessor,
DbSnpVcfProcessor dbSnpVcfProcessor,
bool detectCnvDefault,
TabixWrapper tabixWrapper, ICommandManager commandManager)
{
_workDoer = workDoer;
_sampleSettings = sampleSettings;
_logger = logger;
_executableProcessor = executableProcessor;
_dbSnpVcfProcessor = dbSnpVcfProcessor;
_detectCnvDefault = detectCnvDefault;
_tabixWrapper = tabixWrapper;
_commandManager = commandManager;
}
