Solution:
# BEGIN WordPress
<IfModule mod_rewrite.c>
RewriteEngine On
RewriteBase /
RewriteRule ^index\.php$ - [L]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !^/codeigniter/
RewriteCond %{REQUEST_URI} !^/someothersubdir/
RewriteRule . /index.php [L]
</IfModule>
# END WordPress