/** * Get a variant data reader depending on the type of the input file. * * @param input Stream Input variant file (avro, json, vcf) * @return VariantReader * @throws StorageEngineException if the format is not valid or there is an error reading */ public static VariantReader getVariantReader(Path input) throws StorageEngineException { return getVariantReader(input, null); }
/** * Get a variant data reader depending on the type of the input file. * * @param input Stream Input variant file (avro, json, vcf) * @param metadata Optional VariantSource * @return VariantReader * @throws StorageEngineException if the format is not valid or there is an error reading */ public static VariantReader getVariantReader(Path input, VariantStudyMetadata metadata) throws StorageEngineException { return getVariantReader(input, metadata, false); }
private void loadAvro(String collection, Path path) throws StorageEngineException, IOException, SolrServerException { // reader VariantReader reader = VariantReaderUtils.getVariantReader(path); // TODO: get the buffer size from configuration file int bufferSize = 10000; List<Variant> variants; do { variants = reader.read(bufferSize); insert(collection, variants); } while (CollectionUtils.isNotEmpty(variants)); reader.close(); }
dataReader = VariantReaderUtils.getVariantReader(input, fileMetadata.toVariantStudyMetadata(studyId));
markStdin(); VariantReader reader = getVariantReader(input, metadata.toVariantStudyMetadata(""), stdin); try { metadata = VariantMetadataUtils.readVariantFileMetadata(reader, metadata);
protected Map<String, Variant> readVariants(URI input) throws StorageEngineException, NonStandardCompliantSampleField { VariantReader variantReader = VariantReaderUtils.getVariantReader(Paths.get(input)); variantReader.open(); variantReader.pre(); List<Variant> variants = variantReader.read(1000); VariantNormalizer normalizer = new VariantNormalizer(new VariantNormalizer.VariantNormalizerConfig() .setReuseVariants(true) .setNormalizeAlleles(true)); variants = normalizer .normalize(variants, true); variantReader.post(); variantReader.close(); return variants.stream().collect(Collectors.toMap(Variant::toString, v -> v)); } }
private VariantFileMetadata checkTransformedVariants(URI variantsJson, StudyConfiguration studyConfiguration, int expectedNumVariants) throws StorageEngineException { long start = System.currentTimeMillis(); VariantFileMetadata source = new VariantFileMetadata("6", VCF_TEST_FILE_NAME); VariantReader variantReader = VariantReaderUtils.getVariantReader(Paths.get(variantsJson.getPath()), source.toVariantStudyMetadata(String.valueOf(studyConfiguration.getStudyId()))); variantReader.open(); variantReader.pre(); List<Variant> read; int numVariants = 0; while ((read = variantReader.read(100)) != null && !read.isEmpty()) { numVariants += read.size(); } variantReader.post(); variantReader.close(); if (expectedNumVariants < 0) { expectedNumVariants = source.getStats().getNumVariants(); } else { assertEquals(expectedNumVariants, source.getStats().getNumVariants()); //9792 } assertEquals(expectedNumVariants, numVariants); //9792 logger.info("checkTransformedVariants time : " + (System.currentTimeMillis() - start) / 1000.0 + "s"); return source; }
VariantReader variantReader = VariantReaderUtils.getVariantReader(input, metadata, stdin);
DataReader<Variant> variantReader = VariantReaderUtils.getVariantReader(Paths.get(inputUri), metadata, stdin) .then(duplicatedVariantsDetector) .then(remapIdsTask);
boolean stdin = options.getBoolean(STDIN.key(), STDIN.defaultValue()); VariantReader variantReader = VariantReaderUtils.getVariantReader(input, helper.getStudyMetadata(), stdin); int studyId = helper.getStudyId(); int fileId = Integer.valueOf(helper.getFileMetadata().getId());
VariantReader reader = VariantReaderUtils.getVariantReader(Paths.get(etlResult.getTransformResult().getPath()), new VariantFileMetadata(fileId, "").toVariantStudyMetadata(String.valueOf(studyConfiguration.getStudyId())));