[WIP] Decontamination filter for khmer

Hi @mr-c,

As promised, I've started to tackle issue #232. Just got started, I'm figuring out how khmer for now, so not much to see here yet (see XXX's), but I'll be iterating on this PR until it's ready for consumption.

- [x] Is it mergable
- [ ] Did it pass the tests?
- [ ] If it introduces new functionality in scripts/ is it tested?
  Check for code coverage.
- [x] Is it well formatted? Look at `pep8`/`pylint`, `cppcheck`, and
  `make doc` output. Use `autopep8` and `astyle -A10 --max-code-length=80`
  if needed.
- [ ] Is it documented in the Changelog?
- [x] Was spellcheck run on the source code and documentation after changes
  were made?

s/read/total/