  Hypergraph product codes are a class of quantum low density parity check
(LDPC) codes discovered by Tillich and Z\'emor. These codes have a constant
encoding rate and were recently shown to have a constant fault-tolerant error
threshold. With these features, they asymptotically offer a smaller overhead
compared to topological codes. However, existing techniques to perform logical
gates in hypergraph product codes require many separate code blocks, so only
becomes effective with a very large number of logical qubits. Here, we
demonstrate how to perform Clifford gates on this class of codes using code
deformation. To this end, we generalize punctures and wormhole defects, the
latter introduced in a companion paper. Together with state injection, we can
perform a universal set of gates within a single block of the class of
hypergraph product codes.
