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Is it possible to add a feature to famitracker to have it interpolate output? It would fix a few issues, like the insufferable pain of constantly starting and stopping the pulses, or the fact that the direct output seems to have a lot of garbage, which is especially noticeable with an 8-bit sample size.
It's not a large level of garbage, but for me, the audio output (not wav output) seems to contain underlaying white noise. Also, I think I saw something recently showing that there was a little bit of distortion on halts, don't exactly remember where I saw that, though.
There's also some problems I have, personally, with the audio being far too hard to the ears when using just pulse waves.
Ok. The output from famitracker is modeled after the NES hardware and should sound as close as possible to that. If you find that unpleasant then you could try changing the filtering settings, but beside that there is nothing more to do.
But if you notice differences between audio output and WAV export then you probably have some problems with your sound drivers, because both should be identical.