visitor: use ACTION_ASSEMBLY_GET_VERTEX_AND_SET_VISITOR_FLAG on main vertex

Link: https://github.com/GeneAssembly/biosal/issues/836
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>
assembly_graph_store: set flag when action is ACTION_ASSEMBLY_GET_VERTEX_AND_SET_VISITOR_FLAG

Link: https://github.com/GeneAssembly/biosal/issues/836
Signed-off-by: Sébastien Boisvert <boisvert@anl.gov>