This week's book giveaway is in the OCAJP 8 forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide and have Edward Finegan & Robert Liguori on-line! See this thread for details.
If this was my problem in Java I would consider two solutions:
1. for a small input stream - read the whole thing into a byte and create a new input stream that starts in the right place to pass to the transformer.
2. for a big input stream - write a InputStream extension class that skips to the valid start when initialized.