Fixes to assembler to get simple SNP calling working.

Some basic cleanup on the assembler to get SNP calls cleaned up. This commit adds several tests, cleans up de Brujin graph creation and variant emittance, and starts to clean up HMM alignment. Follow on work will focus on:

* Cleaning up HMM alignment/scoring for indels
* Cleaning internal assembler data structures

This is identical to #27, except the pull request has been rebased down to a single commit, and the pull request is against master. I have deleted the topic branch.