There are a number of binary formats, this format is Scott Crosby's binary format based on Google's protobuf.
To make use of this reader you must have the java protobuf library as well as Scott's OSM-binary package http://github.com/scrosby/OSM-binary
The format is a storage format designed to be quicker and smaller than the XML format but preserve the element ordering and features of that format. We can therefore pretty much re-use most of the code that is used for reading the XML format.