Start working on 2.3 release
Rename directory
Update pbalign call
Remove deprecated chemistry loading workflow
Override scripts

Add modified scripts that override functionality provided by the secondary
installations.
Rename directory python -> scripts
Update to conform to 2.3 SW stack
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.
Checkpoint

Works mechanically end-to-end.  Still experimenting with chunk
arrangments and alignment stream processing. Correction not quite
working as expected.
Ready for tests on larger genomes

Reworked the correction pipeline to be target oriented, works a bit
better now with chunking.  The dextract code does not take into
consideration the hole type so may include problematic reads from things
like fiducials, may consider going back to pls2fasta.
Checkpoint for dazzler integration

Got most of the block logic worked out.  There is a problem where
daligner segfaults when 'DBsplit -a' is used.  I fixed a few problems
where uninitialized variables were getting initialized elsewhere.  Don't
want to spend too many cycles figuring out to fix, so will try to work
with the 'garden path' that retains only the longest subreads.

Adapter code basically working, though somewhat slow.
Adding a new circular check recipe

Note, this does not actually circularize, rather just checks whether or
not a single sequence 'looks circular'.
Update to handle multi-fasta file

Can now pass it a fasta file with 1 or more sequences.  Will skip any
sequences that are less than 2*$(OVLSIZE).  Prints out a message if any
sequence looks circular.
Uncomment .INTERMEDIATE

Clean up after ourselves (except for the output directory)
Add informative comments to circular.mk

Includes usage and caveats.
Rename circular.mk to circularize.mk so it isn't confused with CCS
Add ccs makefile
Merge pull request #1 from dalexander/2.3.0-ccs

2.3.0 ccs