Fixes to HMM/Haplotype code to correct indel calling.
Merge pull request #49 from fnothaft/assembler-basic-indels

Fixes to HMM/Haplotype code to correct indel calling.
parameterize hmm; split out functions; add alignment state
Merge pull request #50 from hammerlab/parameterize-hmm

Parameterize HMM
update refid to use refname instead; add broadcast to bqsr call
Merge pull request #51 from hammerlab/adam-update

Update refid to use refname instead
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