Yoga does not have to involve working with the chakra. In fact, some yoga texts just skim over the chakras and a few don't even mention them at all.
Your yoga teacher most likely will not incorporate chakra exercises. Some systems of yoga do not work with the chakras, while others, such as tantra and kundalini yoga, work extensively with the chakra energy. Your teacher may incorporate the chakra points in a meditation or perhaps mention them He or she might ask you to visualize or focus on a particular area of the body that is troubling you.