Marcus Johnson wrote:

> is it on a per subframe basis, and if so, is each frame padded if
> it’s not a multiple of 512 bits? or do I have to decode all the data,
> and run it over the decoded file at once?

Documentation is here:

     https://xiph.org/flac/documentation_format_overview.html

MD5SUM is of the un-encoded audio data and of the whole stream.

Erik
-- 
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Erik de Castro Lopo
http://www.mega-nerd.com/
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