Keep Coding

I've recently started porting the C implementation of my project to the NIOS II system and I seem to have hit a snag. My original implementation uses file operations (fopen, fscanf, fgets,etc.). However I'm using the University Program IP Core and therefore have to use the HAL functions provided by Altera.
So the question is, will I have to rewrite the portions where I read in formatted text and read byte by byte and then format? Or is it possible to keep my current code?
PS
I am using Quartus II 13.0 with Eclipse Build Tools and my development board is the Altera DE1.
The only solution I could think of is to save my whole text file into an array and then change the formatted file operations to their string counterparts, however this would probably take up a lot of space. I don't think using an OS on the NIOS II is an option for me either.