public DataflowReadEvaluator(GeminiOptions geminiOptions, IGeminiDataSourceFactory dataSourceFactory, GeminiSampleOptions geminiSampleOptions, IGeminiDataOutputFactory dataOutputFactory, IBlockFactorySource blockFactorySource) { _geminiOptions = geminiOptions; _dataSourceFactory = dataSourceFactory; _geminiSampleOptions = geminiSampleOptions; _dataOutputFactory = dataOutputFactory; _blockFactorySource = blockFactorySource; }
public GeminiWorkflow(IGeminiDataSourceFactory dataSourceFactory, IGeminiDataOutputFactory dataOutputFactory, GeminiOptions geminiOptions, GeminiSampleOptions geminiSampleOptions, RealignmentOptions realignmentOptions, StitcherOptions stitcherOptions, string outputDirectory, RealignmentAssessmentOptions realignmentAssessmentOptions, IndelFilteringOptions indelFilteringOptions, ISamtoolsWrapper samtoolsWrapper) { _dataSourceFactory = dataSourceFactory; _dataOutputFactory = dataOutputFactory; _geminiOptions = geminiOptions; _geminiSampleOptions = geminiSampleOptions; _realignmentOptions = realignmentOptions; _samtoolsWrapper = samtoolsWrapper; _stitcherOptions = stitcherOptions ?? new StitcherOptions(); _geminiFactory = new GeminiFactory(geminiOptions, indelFilteringOptions); var bamRealignmentFactory = new BamRealignmentFactory(geminiOptions, realignmentAssessmentOptions, stitcherOptions, realignmentOptions, outputDirectory); _bamRealignmentFactory = bamRealignmentFactory; }
public OutcomesWriter(string outDir, IGeminiDataOutputFactory outputFactory) { _outDir = outDir; _outputFactory = outputFactory; }