I am trying to read chunks of data from a file directly into a struct but the padding is causing too much data to be read and the data to be misaligned.
Do I have to man
You can change padding by explicitly asking your compiler to align structs on 1 byte instead of 4 or whatever its default is. Depending on environment, this can be done in many different ways, sometimes file by file ('compilation unit') or even struct by struct (with pragmas and such) or only on the whole project.