Begin dazzler integration

New makefile integrating daligner into HGAP workflow
Adpater script for daligner results to m4 format
Integration experiments

Almost made it through correction, but turns out that separating out
seed reads just makes things more complicated.  I plan to use whatever
partitioning scheme dazzler uses instead, then extract seed reads from
there.
First cut, basic plumbing working

Needed to add a few more adapter layers:
    - Basic chimeric-like alignment filtering
    - Uppercase the subread bases, minor header modification
    - Fix minor issue with alignment collapsing

Tested on ecoli and got decent results, but needs much more work.