I open my window a small amount...

Flies are attracted to cooler air and light. If at night you have the lights on, you'll attract a **** load of the buggers and eventually some of them will get in. If you're that bothered, a fly net or motion activated napalm will do the trick.
 
Venus Flytrap and Pitcher plant on the window will take care of the problem and give you some nice greenery to look after.
 
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