clean up runpart a bit
cache 5000 simulated seqs for performance comparison

also fix only_genes option in recombinator
remove unused tree-gen.r
add performance plotter

and partially implement the hamming-distance-to-naive stuff
aaaaaaaaaaaaaaaaaaaa

can't get the stupid right hand j deletions to work
stash... need to swap dirs
stash... need to switch to the subsidiary ham dir
Merge branch 'dev' of github.com:psathyrella/ham into dev
several fixes

1) to allow left-hand v deletions and right-hand j ones
2) to be kinda of tolerant of j matches ending before the end of the
query sequence (will still crash it in places)
3) finish adding hamming-to-naive plots
add joinsolver parser

still a work in progress
still working on joinparser

*@#$*$* this shouldn't be so hard
getting there...

almost two hundred *#$@ing lines. *sigh*
still working on joinparser

so

many

special

@*$$U!$ing

cases
ok! hardly ever failing now

just need to add perfplotter
*phew* all working

now if I could just convince the darn web site to process more than a
couple hundred sequences at a time I could get some decent plots
Tidying readme.

(note markdown syntax)
start working on imgt parser
Merge branch 'master' of github.com:psathyrella/ham into dev

Conflicts:
	readme.md
arg subtree broke the readme
add section to readme