public void GetItems() { using (var reader = new RefMinorReader(new StreamReader(GetStream()), GetSequenceProvider())) { var items = reader.GetItems().ToList(); Assert.Equal(3, items.Count); } }
private static ExitCodes ProgramExecution() { var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference)); var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version"); string outFileName = $"{version.Name}_{version.Version}_{SaCommon.RefMinorTag}".Replace(' ', '_'); using (var refMinorReader = new RefMinorReader(GZipUtilities.GetAppropriateStreamReader(_inputFile), referenceProvider)) using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.RefMinorFileSuffix))) using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.RefMinorFileSuffix + SaCommon.IndexSufix))) using (var writer = new RefMinorDbWriter(new ExtendedBinaryWriter(nsaStream), new ExtendedBinaryWriter(indexStream), version, referenceProvider, SaCommon.SchemaVersion)) { writer.Write(refMinorReader.GetItems()); } return(ExitCodes.Success); }
public void LoopBack() { var version = new DataSourceVersion("onekgen", "v0.3", DateTime.Now.Ticks); using (var reader = new RefMinorReader(new StreamReader(GetStream()), GetSequenceProvider())) using (var stream = new MemoryStream()) using (var indexStream = new MemoryStream()) using (var writer = new RefMinorDbWriter(new ExtendedBinaryWriter(stream), new ExtendedBinaryWriter(indexStream), version, GetSequenceProvider(), SaCommon.SchemaVersion)) { writer.Write(reader.GetItems()); stream.Position = 0; indexStream.Position = 0; using (var dbReader = new RefMinorDbReader(stream, indexStream)) { Assert.Equal("T", dbReader.GetGlobalMajorAllele(ChromosomeUtilities.Chr1, 15274)); Assert.Null(dbReader.GetGlobalMajorAllele(ChromosomeUtilities.Chr1, 1524)); } } }