move haplotype to separate classes
Merge pull request #47 from hammerlab/move-haplotype

Move haplotype to separate classes
Fix scheme not found issue with HDFS
Merge pull request #48 from hammerlab/hdfs-fix

Fix scheme issue with HDFS
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
Merge pull request #46 from hammerlab/kmer-fixes

Refactor KmerGraph creation