public static Query parseQuery(StorageVariantCommandOptions.VariantQueryCommandOptions queryVariantsOptions, List<String> studyNames) throws Exception { VariantWriterFactory.VariantOutputFormat of = VariantWriterFactory.toOutputFormat(queryVariantsOptions.outputFormat, null); return parseGenericVariantQuery(queryVariantsOptions, queryVariantsOptions.study, studyNames, queryVariantsOptions.commonQueryOptions.count, of); }
public static OutputStream getOutputStream(String output, String outputFormatStr) throws IOException { VariantOutputFormat outputFormat = toOutputFormat(outputFormatStr, output); return getOutputStream(output, outputFormat); }
.toOutputFormat(variantQueryCommandOptions.outputFormat, variantQueryCommandOptions.commonQueryOptions.output); variantStorageEngine.exportData(uri, of, query, options);