public void export(@Nullable URI outputFileUri, VariantOutputFormat outputFormat, Query query, QueryOptions queryOptions)
throws IOException, StorageEngineException {
String outputFile = null;
if (outputFileUri != null) {
outputFile = outputFileUri.getPath();
}
outputFile = VariantWriterFactory.checkOutput(outputFile, outputFormat);
try (OutputStream os = VariantWriterFactory.getOutputStream(outputFile, outputFormat)) {
boolean logProgress = !VariantWriterFactory.isStandardOutput(outputFile);
exportData(os, outputFormat, query, queryOptions, logProgress);
}
if (metadataFactory != null && !VariantWriterFactory.isStandardOutput(outputFile)) {
VariantMetadata metadata = metadataFactory.makeVariantMetadata(query, queryOptions);
writeMetadata(metadata, outputFile + METADATA_FILE_EXTENSION);
}
}