Removed unnecessary Element reference SubClass, which was propably the cause for 

java.lang.ClassCastException: org.vesalainen.bcc.SubClass cannot be cast to com.sun.tools.javac.code.Symbol$ClassSymbol
Changed generated class to be resource rather than JavaFileObject. when generated class was JavaFileObject, the new class processed for annotations. This caused AssertionError because processed class already existed...

Maybe I should generate the code in existing class???