I have some .ogg sound files that must be merged together.But the problem is in that the java only support .wav extension (as I used AudioSystem and AudioInputStream).
I've searched among different pages for converting and I've not found a better way than.
Do you know a better way other than using Command line tool?
I think you may have to inspect and tinker with the source code. This can be obtained from various libraries that have JOrbis and other files needed for ogg playback and encoding (there are several on github).
For a project where I needed to load decompressed ogg files (that were originally wav) into memory, I used source code from the example OggPlayer (usually included in the package) and intercepted the bytes before they were written to a SourceDataLine. You can maybe also find a hook in example code that compresses wav to ogg and then link the two parts.