in reply to Comparing Two Audio Files
I'm not an expert on either, but I'd probably take a stab at problem A (matching noisy recordings) by first applying a low-pass filter to get rid of most of the noise, then downsample to some really low sample-rate, then find the peaks in the recording and see if the timing of the peaks matches any of the pre-determined messages.
That would probably only work if you have a fairly limited number of messages, but at least it's reasonably easy to implement using standard command-line driven audio tools for the conversions and then using something like Audio::SndFile (disclaimer: I wrote it) to parse the data and find the peaks.
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