Thanks for the reply.
Your solution works about twice as fast as a perl on-liner someone gave me, but I lost 21 bits along the way somewhere. The size of my source file and perl solution result file were the same, but 21 bits less using the tr command above. It's a 38 meg file, so it's not like its a line feed or something.
Hmmm. Weird.
I think I'll try a diff on it and see what happened.