Optional loadIndex()

in S3HtsjdkPlugin/src/main/java/com/epam/cmbi/s3/IndexLoader.java [57:81]

• 21 lines of code
• 3 McCabe index (conditional complexity)

    Optional<SeekableStream> loadIndex(AmazonS3URI bamURI) throws IOException {
        LOG.info("Trying to set index file for " + bamURI.toString());
        Optional<AmazonS3URI> index = providedIndexURI()
                .map(Optional::of)
                .orElseGet(() -> nearbyIndexURI(bamURI));

        if (!index.isPresent()) {
            LOG.info("Index wasn't provided for " + bamURI.toString());
            return Optional.empty();
        }

        LOG.info("Start download index: " + index.get());
        AmazonS3URI indexURI = index.get();
        S3InputStreamFactory streamFactory = new S3InputStreamFactory(client);
        InputStream stream = streamFactory.loadFully(indexURI);
        long fileSize = client.getFileSize(indexURI);
        byte[] buffer = IOUtils.toByteArray(stream);

        if (fileSize != buffer.length) {
            throw new IOException("Failed to fully download index " + indexURI);
        }

        LOG.info("Finished download index: " + index.get());
        return Optional.of(new SeekableMemoryStream(buffer, indexURI.toString()));
    }