WordPress alongside Codeignitier?

I have ci installed in root and wordpress inside wordpress directory.
I already allowed wordpress to use root by setting site url and main .htaccess to rewrite wordpress directory, but because ci is inside root i have url conflict between ci and wordpress..
You know that ci using pretty links, so when i try to run this for example:

example.com/ci_class/ci_function

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It’s redirects me to wordpress template with message

Not Found

This happens probably because i included wordpress wp-load.php inside index.php of codeignitier…

What i can to do?
I want to use wordpress functions inside ci, but i also want that ci url works fine…

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