Encryption problem with CipherInputStream/CipherOutputStream

Hi I have the following code I tested to encrypt/decrypt file and all is go=
od. It works correctly for full file encryption and now I want to test part=
ial encryption of 100000 bytes. I tried read the 100000 from a text file fu=
ll of "qwerty" text and encrypt it in another file and I am able to decrypt=
 this file back to the 100000 bytes of "qwerty" output to a new test file.

So it seems like the partial encryption is ok, all I need is implement Ciph=
erInputStream to decrypt the first 100000 bytes write to a output file and =
do a normal FileInputStream and write to the output write. Theoretically I =
should have implemented the partial file encryption/decryption.

Now, when I open the output file, I saw unreadable character at EOL. What i=
s wrong, how can I correct it?

EOF -> "qwertyqwertyqwertyqwertyqwertyqwerty=B1=84w'=E7=F8]uX\=9CaQ2=CBI=F5=
=93=DC=B1=F5=FE=CB=DCTN=B3'"

Cheers.

    public static void encryptFile(SecretKey key, File sourceFile,
            File secretFile) throws Exception {
        byte[] salt = new byte[8];
        Random random = new Random();
        random.nextBytes(salt);
 
        final int BUFF_SIZE = 100000;
        final byte[] buffer = new byte[BUFF_SIZE];
 
        PBEParameterSpec spec = new PBEParameterSpec(salt, ITERATIONCOUNT);
        Cipher cipher = Cipher.getInstance(ALGORITHM2);
        cipher.init(Cipher.ENCRYPT_MODE, key, spec);
 
        InputStream in = null;
        OutputStream out = null;
        in = new FileInputStream(sourceFile);
        out = new FileOutputStream(secretFile);
        CipherOutputStream cos = new CipherOutputStream(out, cipher);
 
        try {
            out.write(salt);
            boolean pEncrypt = true;
            while (true) {
                synchronized (buffer) {
                    int amountRead = in.read(buffer);
                    if (amountRead == -1) {
                        break;
                    }
                    if (pEncrypt) {
                        cos.write(buffer, 0, amountRead);
                        pEncrypt = false;
                    } else {
                        out.write(buffer, 0, amountRead);
                    }
                }
            }
        } finally {
            if (in != null) {
                in.close();
            }
            if (cos != null) {
                cos.close();
                out.close();
            }
        }
    }
 
    public static void decryptFile(SecretKey key, File secretFile,
            File decryptFile) throws Exception {
        byte[] salt = new byte[8];
 
        final int BUFF_SIZE = 100000;
        final byte[] buffer = new byte[BUFF_SIZE];
 
        InputStream bis = null;
        OutputStream out = null;
        bis = new FileInputStream(secretFile);
        out = new FileOutputStream(decryptFile);
 
        bis.read(salt);
 
        PBEParameterSpec spec = new PBEParameterSpec(salt, ITERATIONCOUNT);
        Cipher cipher = Cipher.getInstance(ALGORITHM2);
        cipher.init(Cipher.DECRYPT_MODE, key, spec);
 
        CipherInputStream in = new CipherInputStream(bis, cipher);
 
        int b = 1;
        Boolean pEncrypt = true;
        while (true) {
            synchronized (buffer) {
                if (pEncrypt) {
                        b = in.read(buffer);
                        pEncrypt = false;
                } else {
                    b = bis.read(buffer);
                }
                if (b == -1) {
                    break;
                }
                out.write(buffer, 0, b);
            }
        }
        out.close();
        bis.close();
        in.close();
    }