fix directory name and --sequence_name value
Change sequenceName back to just '1'
Update v1beta jar one last time
Upgrade to v1beta2 and fix compile errors
Rename classes and commands to match v1beta2
Update readme to v1beta2
Rename SearchCallsetsCommand.java to SearchCallSetsCommand.java

Somehow this didn't get picked up correctly from my local client...
Rename SearchCallsetsCommandTest.java to SearchCallSetsCommandTest.java
Update library version
Add support for the align* APIs
Fix command descriptions

Fix typo in read_group_set
Add support for variant calling
Check in v1beta2 jar
Improve help messages with explicit usage