read file in classpath

Change . to / as the path separator and use getResourceAsStream:

reader = new BufferedReader(new InputStreamReader(
    getClass().getClassLoader().getResourceAsStream(
        "com/company/app/dao/sql/SqlQueryFile.sql")));

or

reader = new BufferedReader(new InputStreamReader(
    getClass().getResourceAsStream(
        "/com/company/app/dao/sql/SqlQueryFile.sql")));

Note the leading slash when using Class.getResourceAsStream() vs ClassLoader.getResourceAsStream.
getSystemResourceAsStream uses the system classloader which isn’t what you want.

I suspect that using slashes instead of dots would work for ClassPathResource too.