Adding k-mer and q-mer counting.
Merge pull request #269 from fnothaft/count-kmers-qmers

Adding k-mer and q-mer counting.
Created command categories
Fixes issue in reference models where strings are not sanitized on collection from avro.
Merge pull request #272 from karenfeng/command-categories

Created command categories
Merge pull request #273 from fnothaft/sanitize-reference-name

Fixes issue in reference models where strings are not sanitized on collection from avro.