move misc/align.py into scripts/bealign, as a replacement for hy454/aligner, leverage lazypar fork of joblib for stream evaluation
make bealign more like aligner, misc refinements to SamIO and BamIO (write() returns count of records written)
do not print header without records in SamIO, raise issues in aligner when len(reference) is not a multiple of 3, listen to NCPU env var in bealign
compile fixes for aligner, bam2msa script, and gapless in BioExt.misc for stripping gaps
position starts at 1 in BAM files
fix default value thinko in bealign script
handle empty query sequences gracefully, new strip_insertions function for bam2msa script, letter indexing into ScoreMatrix, and constify tables in CodonAlignStringsStep
add the reverse complement ability to bealign
use pysam for reading/writing from/to SAM and BAM files, consensus script, quiver module, extinguish trailing Ns in Aligner
fix issues with Aligner on 2.7, add custom joblib to make things easier, and most importantly, the new custom merger code
add ndarray as I have it in setup.py now too....
get merger mostly working
fix py2.7 errors with bealign, and add a progress indicator into bealign
fix a pretty serious error in bealign: it wasn't handling the HY_111_011 case correctly, there was a typo in _compute_codon_matrices()
fiddle a few things to improve codon-aware alignment, disable consensus until I can figure out how to fix the problem with Illumina data
parenthesis for paranoia
fix forgotten modules
add graphing modules
update rateclass machinery from sequtil
fix missing includes in rateclass.cpp