Upgrade of trim-low-abund for better, more profitable streaming.

Support for k-mer spectral error analysis, sublinear error profile calculations from shotgun data sets (sandbox/calc-error-profile.py), adaptive variant collection based on graphalign (sandbox/collect-variants.py), streaming error correction (sandbox/correct-errors.py), and streaming error trimming (sandbox/trim-low-abund.py).  The k-mer spectral error analysis and error profile/trimming is part of the 2014-streaming paper (https://github.com/ctb/2014-streaming).
On Sun, Dec 14, 2014 at 12:31:45PM -0800, Michael R. Crusoe wrote:
> > +            ##
> > +
> > +            # build the alignment...
> > +            score, graph_alignment, read_alignment, truncated = \
> > +                aligner.align(record.sequence)
> > +
> > +            # next, decide whether or to keep it.
> > +            keep = False
> > +            if truncated:
> > +                keep = True             # keep all truncated alignments - why?
> > +            else:
> > +
> > +                # build a better sequence -- this is the corrected one.
> > +                if True:
> > +                    graph_seq = graph_alignment.replace("-", "")
> > +                else:
> 
> Lets remove the uncallable code path before merging

It's a reminder that I still don't understand what the right approach is -
would prefer to leave it in as ugly code until we deal with the whole script.