In about two weeks, I plan to land 
this CL, which removes three 
CreatePeerConnectionFactory() overloads and one 
CreatePeerConnectionFactoryWithAudioMixer() overload—precisely the ones that 
don't take explicit 
AudioEncoderFactory and 
AudioDecoderFactory arguments.
In order to keep exactly the current behavior, call CreateBuiltinAudioEncoderFactory() and CreateBuiltinAudioDecoderFactory() and pass in their return values. However, if you want control of the set of codecs being used, you also have the option to use CreateAudioEncoderFactory<...>() and CreateAudioDecoderFactory<...>() instead. (The ... in the template parameters is where you explicitly list the codecs that you want.)
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