Added top dirs
Added source dir.
added comments
Added suggestion for future code
Added some print statements
Added support for start, end alignment coordinates for list. Also changed list file names to have names in chrX format.
added a createCSIndexesOnSpeciesPosition function. Also added support for dynamically generating table spec so post prob tables can contain any number of states.
Added sorting of the created maf entries on the part of the name before the first '.'.
Fixed a bug so we now test sorted lists of species names.
Fixed typos and added support for start, end list coordinates.
Added a chunkFilePrefix keyword arg to __init__ of PyTablesOutput. Changed to skipping generation of coordinates for other than the reference species.
Changed to sorted iteration over table.
Fixed a bug that prevented printing of the last line of seq if this was 100 long.
Added ez_setup as external and added a setup.py script
Fixed so sorting of maf is not relevant
Added support for empty mafs and fixed a small bug
Added the file CoalhmmPipeline/MafJunkContentQualityFilter.py
Added check for empty maf and added specifiation of junkchars (not just N hardcoded)
Added specification of junkchars
Added support for specifying a maximum size of chunks after joining