use function from adam to create reference sequence
Merge pull request #53 from hammerlab/build-reference

Use function from ADAM to create reference sequence
refactor kmer graph creation
Merge pull request #46 from hammerlab/kmer-fixes

Refactor KmerGraph creation
simplify haplotype queue creation
Merge pull request #55 from hammerlab/haplotype-hmm-simpler

Simplify haplotype queue creation
refactor hmmaligner