stash -- not working yet but have waaaaaay to many changes
grrr.... I've broken *something* but I'm not quite

sure what it is yet...
fix bug in hmm model file checker

I really, really, *really* wish I could say that was the first time I'd
removed elements of a list while I was iterating over 'em.
v_right removal effective erosions  seem work

but still testing, and still need to remove a few leftover v_right things
little clean ups
fix up error messages
oops missed staging runpart.py on last commit
seems to work... except the bam merge

so I'm stashing before I rewrite to just loop over the output files
finish single-machine parallel. for smith-waterman
update parameter cache
add to todo