Checked out graphalign branch from jason, first pass at resolving conflicts.  Need to make sure conflicts were resolved correctly\!
Added read_aligner classes DOESN'T WORK YET
It compiles, and sort of works
Resolved conflict with makefile
Working (if threadbare) implementation of aligning reads to the DBG based on Jason Pell's work
Updated aligner.o => read_aligner.o
Added a null model and bits saved check to prevent opening 'bad' nodes.  Started on a little code standards compliance.
Added a few todo notes so they're written down instead of all in my head
Merged with ged master branch
More notes in read_aligner.hh
Added (and commented out) support for bidirectional alignment
Added trusted coverage threshold and bits saved theta (tuning parameter for truncating alignments) to the read aligner and python api
Real, working read-graph alignment algo with diginorm script
Added code to free up memory allocated in the ReadAligner
Merged with ged master
Modified setup.py to build the new read_aligner and added a namespace prefix to a random BoundedCountingType in _khmermodule that was missing it
Updated the read aligner tests for the new aligner implementation
Experimenting with new probabilites for the alignment model (commented out score comparison in test until finalized)
Improvements and bug fixes to the read aligner, read aligner tests disabled until the probability model is 'finalized'
merge with upstream