public void OneRcv_oneVcv() { var sequenceProvider = GetSequenceProvider(GenomeAssembly.GRCh37, 31496350, "C"); var reader = new ClinVarReader(FileUtilities.GetReadStream(Resources.ClinvarXmlFiles("RCV000124712.xml")), FileUtilities.GetReadStream(Resources.VcvXmlFiles("VCV000137106.xml")), sequenceProvider); var items = reader.GetItems().ToArray(); Assert.Equal(2, items.Length); }
private static ExitCodes ProgramExecution() { var version = DataSourceVersionReader.GetSourceVersion(_rcvFile + ".version"); string outFileName = $"{version.Name}_{version.Version}"; using (var referenceProvider = new ReferenceSequenceProvider(FileUtilities.GetReadStream(_compressedReference))) using (var clinvarReader = new ClinVarReader(GZipUtilities.GetAppropriateReadStream(_rcvFile), GZipUtilities.GetAppropriateReadStream(_vcvFile), referenceProvider)) 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.ClinvarTag, false, true, SaCommon.SchemaVersion, false)) using (var schemaStream = FileUtilities.GetCreateStream(Path.Combine(_outputDirectory, outFileName + SaCommon.SaFileSuffix + SaCommon.JsonSchemaSuffix))) using (var schemaWriter = new StreamWriter(schemaStream)) { nsaWriter.Write(clinvarReader.GetItems()); schemaWriter.Write(clinvarReader.JsonSchema); } return(ExitCodes.Success); }