Make mkNodeGraph ignore edges to non-present nodes

Change the behavior of mkNodeGraph to tacitly ignore all instances
where one of the nodes is not in the list of nodes. In this way, we
can construct sub-graphs by filtering the nodes and ignoring any
possibly added isolated nodes for the missing indexes.

Signed-off-by: Klaus Aehlig <aehlig@google.com>
Reviewed-by: Guido Trotter <ultrotter@google.com>