Adding code to align reads with SNAP.
Refactoring transition matrix to allow for cleaner configuration, and adding more config details to assembler.
Merge pull request #72 from fnothaft/snap

Adding code to align reads with SNAP.
Merge pull request #74 from fnothaft/model-split

Refactoring transition matrix to allow for cleaner configuration
Updated to ADAM 0.10.1-SNAPSHOT stream. Fixed issue with genotype output.
Merge pull request #75 from fnothaft/general-fixes

Upgrade to ADAM 0.10.1-SNAPSHOT stream