Updated avocado to move to org.bdgenomics, and to move to ADAM 0.8.1-SNAPSHOT.
Merge pull request #38 from fnothaft/bdg-0.8.0

Updated avocado to move to org.bdgenomics, and to move to ADAM 0.8.1-SNAPSHOT
move all files to proper package directory
Merge pull request #40 from hammerlab/move-package

Move all files to proper package subdirectory
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