How to stop a thread waiting in a blocking read operation in Java?

I have a thread that executes the following code:

public void run() {
    try {
        int n = 0;
        byte[] buffer = new byte[4096];
        while ((n = in.read(buffer)) != -1) {
            out.write(buffer, 0, n);
            out.flush();
        }
    } catch (IOException e) {
        System.out.println(e);
    }
}

where in is System.in. How can I stop such thread gracefully? Neither closing System.in, nor using Thread.interrupt appear to work.