Added in my modified version of the CD-HIT app controller
Since Pycogent's main repository is slow in the uptake of pull
requests this file is added in for compatibility with the standard
pycogent 1.5.3 release, rather than my development version
Added in an introduction and changed some of the options to bring things inline with recent changes
Added in synonyms and automatically decompress output files
Added in a synonyms dict
added in a synonyms dict and moved the _categories to be an instance variable rather than class
Added in defults for mapping_similarity_cutoffs and preassemble_clustering
added in support for multiple bands of mapping similarity
Added in a compressed result path class for dealing with gzip files
added more generalized interface to set bowtie params
added velvet and fermi assemblers
write in joining code for dealing with different assemblers and multiple mapping strategies
Version update - new assembly options and differential mapping stringencies