private void fillMissing() throws StorageEngineException { StorageVariantCommandOptions.FillMissingCommandOptions cliOptions = variantCommandOptions.fillMissingCommandOptions; ObjectMap options = storageConfiguration.getVariant().getOptions(); options.put(VariantStorageEngine.Options.RESUME.key(), cliOptions.resume); options.putAll(cliOptions.commonOptions.params); variantStorageEngine.fillMissing(cliOptions.study, options, cliOptions.overwrite); }
public void fillMissing(String studyStr, boolean overwrite, ObjectMap config, String sessionId) throws CatalogException, IllegalAccessException, InstantiationException, ClassNotFoundException, StorageEngineException { String userId = catalogManager.getUserManager().getUserId(sessionId); Study study = catalogManager.getStudyManager().resolveId(studyStr, userId); DataStore dataStore = getDataStore(study.getFqn(), sessionId); VariantStorageEngine variantStorageEngine = storageEngineFactory.getVariantStorageEngine(dataStore.getStorageEngine(), dataStore.getDbName()); variantStorageEngine.fillMissing(study.getFqn(), config, overwrite); }
getResourceUri("gaps/file2.genome.vcf"))); variantStorageEngine.fillMissing(studyConfiguration.getStudyName(), new ObjectMap(), true); VariantHadoopDBAdaptor dbAdaptor = (VariantHadoopDBAdaptor) variantStorageEngine.getDBAdaptor(); printVariants(studyConfiguration, dbAdaptor, newOutputUri());
@Test public void calculateStatsMultiCohortsAfterFillMissingTest() throws Exception { VariantStorageEngine storageEngine = getVariantStorageEngine(); storageEngine.fillMissing(studyConfiguration.getStudyName(), new ObjectMap(), false); VariantHbaseTestUtils.printVariants(getVariantStorageEngine().getDBAdaptor(), newOutputUri(getTestName().getMethodName())); calculateStatsMultiCohortsTest(); }