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
Tidying readme.

(note markdown syntax)
arg subtree broke the readme
add section to readme
modify readme
test hipchat integration
Add pair HMM example

Also clean up sequence labels the example yamels.
yamel trimming
Ban the bomb.
Zapping trailing whitespace.
Merge commit '365ec7d237d08bd4042e56e09d5aa87804208634'

Conflicts:
	ham/readme.md