version 0.2

    - emirge.py now uses sparse matrices (scipy) for its major data
    structures (likelihood and posteriors).  This has resulted in a major
    reduction in memory usage, at essentially no change in computation
    time.  Some parts of the code run slower than before, but some run
    faster, and on average, for a typical run, you should see a huge drop
    in memory usage and perhaps a slight speedup.
    - Updated README file
    - Added preprocessed SSU_candidate_db.fasta.gz for convenience
Changed emirge.py to use uclust v4

Tested output with USEARCH 4.0.38, and it is equivalent with old
results with code that used uclust v. 3.x
version 0.21

* Improvements have been made in the merging code that led to a 2-orders-of-magnitude speed-up in merging two sequences together.  Code is now consistently faster than before sparse matrix implementation, while maintaining low memory footprint.
* Since last version tag, this code also now runs with usearch v 4.0.38.  No longer supports uclust v 3.*
Removed os.fsync that was causing problems for some people
A little bit of general cleaning up
-  Rewrote substantial part of the code with aim of making likelihood calculation faster.  Moved some of the likelihood calculation to Cython.  The likelihood function now typically takes < 1/2 the time it used to, and iterations as a whole typically see a speed up of roughly 150 to 200  percent.
-  Added setup.py script to aid in building Cython C module (_emirge.so), and to install emirge.
-  Modified README.txt to indicate that Cython is now a dependency (it already was implicitly for pysam) and to give quick installation instructions.
fixed goof in setup.py for build_ext --inplace
Wrote Cython code for looping over bamfile_data in ProbN calculation.  Speedup 2X to > 10X on some iterations
another minor speed tweak to ProbN calculation.
updated to use uclust version 4.2 which saw a change in command line params and output that had disabled merging.  Also moved some of merging code to Cython for speed.
More tweaking of uclust version 4.2 parameters for merging code.
Added a dependency check for correct usearch version
More tweaking of usearch command line.  Now using iddef 2, as separate sequences from forward and reverse reads in SSU database were not merging properly
Retooled read_bam to reuse information from previous iterations, which results in faster iterations.  This required changing some of the data structures that cache bamfile information (most notable: self.bamfile_data, self.reads, self.quals, self.readlengths)
Moved bamfile iteration over predata to Cython (another speedup)
- Major revision to code splitting out new minor strains, resulting in a big decrease in the time per iteration spent writing out new consensus sequences.
- No longer sorting and indexing bam files each iteration.  This was purely for debugging purposes, and slowed down each iteration.
more (smaller) speed gains in likelihood and probN calculations by moving external looping to Cython functions.
testing new expected_coverage_thresh to try and keep from splitting sequences out with little read support
Added ability to run EMIRGE with just single-end reads (use only -1 without -2).

Note that while I have done some testing on this and it seems to produce reasonable results, EMIRGE with single-end reads has not been as extensively tested as EMIRGE run with paired-end reads.
updated README with single-end note and setup.py to install emirge_rename_fasta.py