Here is the code section that applies it is from the 2006 IRC. The middle 1/3 can be drilled as long as the other rules for drilling are followed the restiction on the middle 1/3 is only for notching.As you can see I split the section in half the first half is all about notching that is where the 1/3 restiction is the second half is for drilling.

R502.8.1 Sawn lumber. Notches in solid lumber joists, rafters and beams shall not exceed one-sixth of the depth of the member, shall not be longer than one-third of the depth of the member and shall not be located in the middle one-third of the span. Notches at the ends of the member shall not exceed one-fourth the depth of the member. The tension side of members 4 inches (102 mm) or greater in nominal thickness shall not be notched except at the ends of the members.

The diameter of holes bored or cut into members shall not exceed one-third the depth of the member. Holes shall not be closer than 2 inches (51 mm) to the top or bottom of the member, or to any other hole located in the member. Where the member is also notched, the hole shall not be closer than 2 inches (51 mm) to the notch.