FLAC or ape spi encode/decode working with audio system?

Has anybody got a flac or monkey's audio spi actually working? I seem to be having problems when I try to getAudioInputStream (works for mp3) and I can't seem to find any examples on how to set it up so that I can encode from PCM to ape or flac.

OK, after much thrashing around it looks like I found a project that does most of what I need. That is cut the files up the way I want to and the ability to simultaneously create different encodings based from the input file. The project is called xuggle. http://www.xuggle.com/ It's reasonably well documented. It uses ffmpeg to do audio and video encoding in a standard manner. It is written in C++. I am assuming it will be faster. It appears to be better documented than the other plugins for the SPI.
Here is a big issue. ffmpeg does not support encoding of monkey's audio, which is a requirement for me, and the java flac implementation SPI does not support flac encoding. My current approach is to exec the encoding of monkey's audio from a command line executable ( like the subsonic project currently does), and use xuggle for everything else.
If anybody has any opinions or suggestions please comment

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FLAC or ape spi encode/decode working with audio system?

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