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I want to cut a video file (i.e. delete parts of it), and do it with the minimum amount of re-encoding possible.

I found this piece of software called Machete, which otherwise works fine, but it makes me set the cut points to key frames. I want to be able to set the cutpoints to any kind of frame I want (which AFAIK means there has to be some re-encoding).

I've tried Avidemux, but it creates broken files if I don't set the cut points to key frames.

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It's non-trivial to write something that will do what you want, but a workaround is to cut the largest chunk possible by key frames and then combine them with the other pieces edited in standard software like virtual dub using a mux tool. – Jan 19 '13 at 1:54
There's no "minimum amount of re-encoding"—there either is, or there isn't. If you cut at intra-frames, it'll work without encoding, of course, and vice-versa. – slhck Jan 19 '13 at 10:49

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