Updates to indel realigner to improve performance and accuracy.
Remove extraneous implicit methods
Merge pull request #314 from fnothaft/indel-realigner-rebase

Updates to indel realigner to improve performance and accuracy.
Merge pull request #320 from genomebridge/remove-implicit-methods

Remove extraneous implicit methods in ReferenceMappingContext
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.