[ADAM-309] Upgrading dependency of bdg-formats to 0.1.2

This commit includes multiple changes:
* 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.
* 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?