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I`m using folliwing code to mux row h264(from android MediaCodec) into .mp4 container
    H264TrackImpl video;
    try {
        video = new H264TrackImpl(new FileDataSourceImpl("/home/aod/tmp/rec_1392309584754.h264"), "eng", 9, 1);
        Movie m = new Movie();
        m.addTrack(video);
        BasicContainer out = (BasicContainer) new DefaultMp4Builder().build(m);
        FileOutputStream fos = new FileOutputStream(new File("/home/aod/tmp/output.mp4"));
        out.writeContainer(fos.getChannel());
        fos.flush();                        
        fos.close();
    } catch ( IOException e) {
        e.printStackTrace();
    }