Reading a writing binary file

I have a binary file with a bit stream I need to modify. I need to change certain bits based on user input. An example in listed below. I can read the data into a byte array, but I'm not sure how to manipulate the data and then write it back out to a file. I need to preserve any leading zeros.

Example File:
00010010101101

Desired File:
10110010101101

Once in a byte array, you can use bitwise operators
Bitwise and Bit Shift Operators (The Java™ Tutorials > Learning the Java Language > Language Basics)