refactor hmmaligner
Merge pull request #52 from hammerlab/hmm-alignment

Refactor HMMAligner and add testing for HMMAligner
get contig length from adamcontig
remove isType methods from variantcall
Merge pull request #59 from hammerlab/drop-contig-length

Get contig length from adamcontig
Merge pull request #60 from hammerlab/drop-type-lookup-methods

Remove is<Type> methods from variantcall