@Override public VariantDBIterator iterator(Query query, QueryOptions options) { try { if (options == null) { options = new QueryOptions(); } options.put(VariantSearchManager.USE_SEARCH_INDEX, VariantStorageEngine.UseSearchIndex.YES); return variantStorageEngine.iterator(query, options); } catch (Exception e) { throw Throwables.propagate(e); } }
public VariantDBIterator iterator(Query query, QueryOptions queryOptions, String sessionId) throws CatalogException, StorageEngineException { String study = catalogUtils.getAnyStudy(query, sessionId); DataStore dataStore = getDataStore(study, sessionId); VariantStorageEngine storageEngine = getVariantStorageEngine(dataStore); catalogUtils.parseQuery(query, sessionId); checkSamplesPermissions(query, queryOptions, storageEngine.getStudyConfigurationManager(), sessionId); return storageEngine.iterator(query, queryOptions); }
VariantDBIterator iterator = variantStorageEngine.iterator(query, options); while (iterator.hasNext()) { Variant variant = iterator.next();
numResults = variantStorageEngine.count(query).first(); } else { try (VariantDBIterator iterator = variantStorageEngine.iterator(query, queryOptions)) { while (iterator.hasNext()) { iterator.next();