It is important to note that this is an IO blocking call. As such, interrupting the thread currently executing this statement will have absolutely no effect.
A clean way of doing this would be to execute this call with an ExecutorService by wrapping it in a Callable implementation. By calling the get(timeout) method on the returned future, you can both control the timeout manually as well as handle interruptions gracefully.
If this thread is interrupted, you will want to close the underlying resource so that the call itself will actually return and you don't leak threads. Something like myInputStream.close().