private static void VerifyFlow(List <ReadPair> reads, GeminiOptions geminiOptions, int expectedRegions)
{
var batchBlockFactory = BatchBlockFactory();
var classificationBlockFactory = new Mock <IClassificationBlockProvider>();
var classifierBlockFactory = ClassifierBlockFactory();
var blockFactory = BlockFactory(batchBlockFactory, classifierBlockFactory, classificationBlockFactory);
var alignments = new List <BamAlignment>();
var mockDataOutputFactory = DataflowMocks.MockDataOutputFactory(alignments);
var mockReader = DataflowMocks.MockReader();
var mockReadPairSource = DataflowMocks.MockDataSource(reads);
var mockDataSourceFactory = DataflowMocks.MockDataSourceFactory(mockReader, mockReadPairSource);
var dataflowEvaluator = new DataflowReadEvaluator(geminiOptions, mockDataSourceFactory.Object,
new GeminiSampleOptions()
{
OutputFolder = "outfoldersample"
}, mockDataOutputFactory.Object, blockFactory.Object);
dataflowEvaluator.ProcessBam();
VerifyCallNumbers(batchBlockFactory, classifierBlockFactory, classificationBlockFactory, mockDataSourceFactory,
blockFactory, expectedRegions);
}
private static void Execute(List <BamAlignment> alignments, List <ReadPair> reads, GeminiOptions geminiOptions, StitcherOptions stitcherOptions, List <ReadPair> lonerpairs = null)
{
var mockOutcomesWriter = new Mock <IOutcomesWriter>();
var mockDataOutputFactory = DataflowMocks.MockDataOutputFactory(alignments);
var mockTextWriter = new Mock <ITextWriter>();
mockDataOutputFactory.Setup(x => x.GetTextWriter(It.IsAny <string>()))
.Returns(mockTextWriter.Object);
var mockReader = DataflowMocks.MockReader();
var mockReadPairSource = DataflowMocks.MockDataSource(reads, lonerpairs);
var mockDataSourceFactory = DataflowMocks.MockDataSourceFactory(mockReader, mockReadPairSource);
var mockSamtoolsWrapper = new Mock <ISamtoolsWrapper>();
var geminiSampleOptions = new GeminiSampleOptions()
{
RefId = 1, OutputFolder = "OutFolder"
};
var geminiWorkflow = new GeminiWorkflow(mockDataSourceFactory.Object, mockDataOutputFactory.Object,
geminiOptions, geminiSampleOptions, new RealignmentOptions(), stitcherOptions, "outdir",
new RealignmentAssessmentOptions(), new IndelFilteringOptions(), mockSamtoolsWrapper.Object);
geminiWorkflow.Execute();
}