|Think about Loose Coupling
I'll have to agree with PJ and adamk here. Checking for each type of newline ending would be horrible, but in a pre-processing situation it might actually speed up the processing time. Another suggestion, not that I'm aware of how the input file is obtained, in the creation of the input file, use a specific newline of your choice to make it uniform and use an output method that would determine what to use when the program is running.
I.E. Program 1 or Section 1 of program takes user input, uses \015 as a standard newline, instead of a system specific newline and creates the input file with that format. Upon use of the input file, the program then spits out system specific newline for "display" of the file.