Update Scalariform to be consistent with ADAM
Run Scalariform
Merge pull request #41 from hammerlab/scalariform-setting

Update Scalariform to be consistent with ADAM
use sequence load instead of only adam load for reference data
Merge pull request #42 from hammerlab/fasta-reference

Use sequence load instead of only adam load for reference data
upgrade adam to 0.9.1-SNAPSHOT and spark to 0.9.1 to fix cli errors
Merge pull request #43 from hammerlab/upgrades

Upgrade adam to 0.9.1-SNAPSHOT and Spark to 0.9.1
homozygous ref and alt were flipped in terms of writing/saving
Merge pull request #44 from hammerlab/reverse-site-calls

Homozygous ref and alt were flipped in terms of writing/saving
refactor kmer graph creation