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My goal was to copy the packages, not to remux them.
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The setpts filters are offset for the slices which have to fade in. The setpts/ asetpts filters are used because trim/ atrim carry over the original timestamps. I have inputted the video multiple times, once for each slice, because using a single input pad (even with split/ asplit) leads to buffer overflows. ffmpeg -i input.mp4 -i input.mp4 -i input.mp4 -i input.mp4 -i input.mp4 \
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Below is the single step command template, assuming five slices.
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