Add --update-method to make_prg update

[leoisl]

Not for this next 0.4.0 release, likely for 0.5.0. Adds a new parameter to make_prg update:

  -m UPDATE_METHOD, --update-method UPDATE_METHOD
                   How to update PRGs. Valid options are (default is careful):
                         exact: update the full PRG's MSA with the new alleles and rebuilds the whole PRG. This method guarantees that the
                                resulting PRG is equivalent to redoing the MSA and rebuilding the PRG from scratch, but it is the slowest method;
                         quick: update just the leaves of the PRG with the new alleles. Alleles that cross leaves are broken into several
                                contained sub-alleles. Although this is the quickest method, it is imprecise when adding long deletions;
                         careful: if there is at least one new allele that cross leaves, then the PRG is updated following the exact method. 
                                  Otherwise, it is updated following the quick method.

Important when we want to study longer variants.

[leoisl]

--update-method quick is what is currently implemented