fixed check_space_for_hashtable to use args.n_tables
Merge pull request #382 from ged-lab/bug/hashtable_size_calculations_wrong

fixed check_space_for_hashtable to use args.n_tables
Removed an extrenuous using namespace khmer; in kmer.hh, fixed resulting errors
Working (if threadbare) implementation of aligning reads to the DBG based on Jason Pell's work

Added python glue code for the read aligner
Added a null model and bits saved check to prevent opening 'bad' nodes.  Started on a little code standards compliance.
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
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'
Modified read aligner script to write out the original sequence when truncated alignments are detected (to be comparable to normalize-by-align.py)
Fixed some bugs in the closed set logic and re-enabled read_aligner tests
Fixed comments in read_aligner.[cc/hh]
Hand merge with fishjord_graphalign & master