Adding code for lifting over between sequences and the reference genome.
Merge pull request #306 from fnothaft/liftover

Adding code for lifting over between sequences and the reference genome.
Upgrading the version of bdg-formats to 0.1.2-SNAPSHOT in the pom.xml
Automated refactoring, renaming all the classes to drop the ADAM prefix.
Starting to fix the field names on Variant and Record types.

In particular, making the following changes:
* updating the (deprecated) uses of Record.end to Record.getEnd
* changing Variant.get/setPosition to Variant.get/setStart
* changing Variant.get/setVariantAllele to Variant.get/setAlterateAllele

The tests still aren't passing, this is mostly due to Indel realignment tests
and I'm not sure why they're not working.  @fnothaft, can you help out a bit here?
Fixing the remaining Variant and Read naming changes, that happened when I rebased.