public void GetItems_test() { var reader = new GlobalMinorReader(GetStream(), _chromDict); var items = reader.GetItems().Cast <ISupplementaryDataItem>().ToList(); var globalMinor = SuppDataUtilities.GetPositionalAnnotation(items); Assert.Equal("{\"globalMinorAllele\":\"G\",\"globalMinorAlleleFrequency\":0.3472}", globalMinor.GetJsonString()); }
private static ExitCodes ProgramExecution() { var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference)); var globalMinorReader = new GlobalMinorReader(GZipUtilities.GetAppropriateReadStream(_inputFile), referenceProvider.RefNameToChromosome); var version = DataSourceVersionReader.GetSourceVersion(_inputFile + ".version"); string outFileName = $"{version.Name}_{version.Version}_globalMinor"; using (var nsaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix))) using (var indexStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.IndexSufix))) using (var nsaWriter = new NsaWriter(nsaStream, indexStream, version, referenceProvider, SaCommon.GlobalAlleleTag, true, false, SaCommon.SchemaVersion, true)) { nsaWriter.Write(globalMinorReader.GetItems()); } return(ExitCodes.Success); }