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Can I use autofocus during pose estimation?

Hi to all, i am developing an iOS app (for iPad) using OpenCV for the ArUco markers detection and pose estimation. Doing the calibration process, i make the estimation of the camera calibration matrix (including the focal length). My question is: during the pose estimation process, do i need to disable the autofocus? I am in doubt because i know that if i change the focal length and then i capture an image, the pose is wrong because the image is taken with a different focal. But on the other hand the autofocus doesn't change really the focal length, isn't? (So it's different for example from the zoom). I am talking about the autofocus system on the iPad, so not a professional camera and i suppose that the autofocus system is software, i mean it make the lenses move backward and forward, but then the "adjustment" is software, am i wrong? Thanks.