Can you just redirect STDIN from the port? So instead of myapp, you invoke myapp < /dev/ttyS0?

Assuming that works, but you want merge the keyboard and barcode reader (so you can use either as an input device), you could write a small program which reads a character from whichever device offers a character first, and then throw that at STDOUT (a reverse version of tee), then pipe this into your program: eet /dev/ttyS0|myapp.

Just a thought... Might well not work