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
arg subtree broke the readme
Merge commit '365ec7d237d08bd4042e56e09d5aa87804208634'

Conflicts:
	ham/readme.md
Merge commit 'a1ff0f9ea212e601e0e8d2552bcea719579f3093' into dev
Merge commit 'c9b952e861fcdb880aaebee7d61d39e1c79c202b'
modify readme