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;
}
