Examples of org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

Package org.broadinstitute.gatk.utils.exceptions

Examples of org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException

org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException
A trivial extension around GATKException to mark exceptions that have been reviewed for correctness, completeness, etc. By using this exception you are saying "this is the right error message". GATKException is now just a catch all for lazy users.

    public static SecureRandom createRandomnessSource ( String randAlgorithm ) {
        try {
            return SecureRandom.getInstance(randAlgorithm);
        }
        catch ( NoSuchAlgorithmException e ) {
            throw new ReviewedGATKException(String.format("Could not find an implementation of the requested random-number generation algorithm %s", randAlgorithm), e);
        }
    }

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            KeySpec keySpec = new X509EncodedKeySpec(rawKey);
            KeyFactory keyFactory = KeyFactory.getInstance(encryptionAlgorithm);
            return keyFactory.generatePublic(keySpec);
        }
        catch ( NoSuchAlgorithmException e ) {
            throw new ReviewedGATKException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
        }
        catch ( InvalidKeySpecException e ) {
            throw new ReviewedGATKException("Unable to use X.509 key specification to decode the given key", e);
        }
    }

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            KeySpec keySpec = new PKCS8EncodedKeySpec(rawKey);
            KeyFactory keyFactory = KeyFactory.getInstance(encryptionAlgorithm);
            return keyFactory.generatePrivate(keySpec);
        }
        catch ( NoSuchAlgorithmException e ) {
            throw new ReviewedGATKException(String.format("Could not find an implementation of the requested encryption algorithm %s", encryptionAlgorithm), e);
        }
        catch ( InvalidKeySpecException e ) {
            throw new ReviewedGATKException("Unable to use the PKCS #8 key specification to decode the given key", e);
        }
    }

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     */
    public static PublicKey loadGATKDistributedPublicKey() {
        InputStream publicKeyInputStream = ClassLoader.getSystemResourceAsStream(GATK_DISTRIBUTED_PUBLIC_KEY_FILE_NAME);


        if ( publicKeyInputStream == null ) {
            throw new ReviewedGATKException(String.format("Could not locate the GATK public key %s in the classpath",
                                                           GATK_DISTRIBUTED_PUBLIC_KEY_FILE_NAME));
        }


        return readPublicKey(publicKeyInputStream);
    }

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            Cipher cipher = Cipher.getInstance(key.getAlgorithm());
            cipher.init(cipherMode, key);
            return cipher.doFinal(data);
        }
        catch ( NoSuchAlgorithmException e ) {
            throw new ReviewedGATKException(String.format("Could not find an implementation of the requested algorithm %s",
                                             key.getAlgorithm()), e);
        }
        catch ( InvalidKeyException e ) {
            throw new ReviewedGATKException("Key is invalid", e);
        }
        catch ( GeneralSecurityException e ) {
            throw new ReviewedGATKException("Error during encryption", e);
        }
    }

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     * @param readBufferSize Number of bytes to read in at one time
     * @return The contents of the file as a byte array
     */
    public static byte[] readFileIntoByteArray ( File source, int readBufferSize ) {
        if ( source == null ) {
            throw new ReviewedGATKException("Source file was null");
        }


        byte[] fileContents;


        try {

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     * @param readBufferSize Number of bytes to read in at one time
     * @return The contents of the stream as a byte array
     */
    public static byte[] readStreamIntoByteArray ( InputStream in, int readBufferSize ) {
        if ( in == null ) {
            throw new ReviewedGATKException("Input stream was null");
        }
        else if ( readBufferSize <= 0 ) {
            throw new ReviewedGATKException("Read buffer size must be > 0");
        }


        // Use a fixed-size buffer for each read, but a dynamically-growing buffer
        // to hold the accumulated contents of the file/stream:
        byte[] readBuffer = new byte[readBufferSize];

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     * @param bytes Data to write
     * @param destination File to write the data to
     */
    public static void writeByteArrayToFile ( byte[] bytes, File destination ) {
        if ( destination == null ) {
            throw new ReviewedGATKException("Destination file was null");
        }


        try {
            writeByteArrayToStream(bytes, new FileOutputStream(destination));
        }

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     * @param bytes Data to write
     * @param out Stream to write the data to
     */
    public static void writeByteArrayToStream ( byte[] bytes, OutputStream out ) {
        if ( bytes == null || out == null ) {
            throw new ReviewedGATKException("Data to write or output stream was null");
        }


        try {
            try {
                out.write(bytes);

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     * @param gzipFile GZIP-format file whose uncompressed size to determine
     * @return The uncompressed size (in bytes) of the GZIP file
     */
    public static int getGZIPFileUncompressedSize ( File gzipFile ) {
        if ( gzipFile == null ) {
            throw new ReviewedGATKException("GZIP file to examine was null");
        }


        try {
            // The GZIP ISIZE field holds the uncompressed size of the compressed data.
            // It occupies the last 4 bytes of any GZIP file:

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