allow gap penalties to be a function of position on reference

[DavidBJaffe]

For some applications, it is desirable that the gap open and gap extend penalties vary
as a function of the position on the target (second) sequence. We encountered this when
aligning a V(D)J transcript to a concatenated V(D)J reference, where we wanted to encourage
gaps at the junction points between the reference segments.

This PR provides a solution that works, but is awkward. In alignment/pairwise/mod.rs,
we add a function custom_with_gap_fns, that is a copy of custom, except that it has two
extra arguments specifying the gap penalties, and each instance of gap_open and gap_extend
in the function are modified accordingly. This is the only change.

The extra arguments are vectors. Ideally they could be closures, although for our application,
vectors are fine. And the code duplication is awful.

It was not clear to us how to implement an elegant solution without breaking the existing
public API (and I'm not sure how to do even that).

Perhaps there is a better solution.

[coveralls]

Coverage decreased (-2.1%) to 85.717% when pulling 1007419 on DavidBJaffe:gap_penalties_as_functions into b6cb869 on rust-bio:master.