bamtools
Revert "bamtools"

This reverts commit 57a3194ed5bdc4fb63a9f6b5731f599dbe84954d.
Revert "Revert "bamtools""

This reverts commit 7be0513263be05bb9da7e5e87feea672228b0f5d.
Merge git://github.com/ekg/clia
Merge git://github.com/ekg/clia
Added construction files
Merge branch 'master' of git://github.com/ekg/clia

Fixes for opt parsing
some constructs & gluing
glue
fixed compile errors
we have alignment

... amazingly random ones.

TODO:
    1) The alignment.  It's wrong.
    2) The DAG construction.  Possibly this is the problem.