[avocado-124] Fixing build issue due to upstream change to ADAM save command.
Merge pull request #124 from fnothaft/fix-build-110714

[avocado-124] Fixing build issue due to upstream change to ADAM save command
[avocado-125] Move to new alignment loader.
Merge pull request #126 from fnothaft/change-loader

[avocado-125] Move to new alignment loader.
[avocado-121] Add a filter to remove reference calls.
[avocado-120] Adding additional statistics output to biallelic genotyper.