Check if two sets have a non-empty intersection

The overhead you are seeing is likely due to function call overhead: op_u is not being inlined.

This version inlines correctly and has the same performance as intersects:

julia> function intersects2(u::DataStructures.IntSet, v::DataStructures.IntSet)
           op_u(x) = u.inverse ? ~x : x
           op_v(x) = v.inverse ? ~x : x

           ch_u, ch_v = u.bits.chunks, v.bits.chunks
           for i in 1:length(ch_u)
               if op_u(ch_u[i]) & op_v(ch_v[i]) > 0
                   return true
               end
           end
           false
       end