New schema, variant context converter changes, and removal of old genotype converter code
Remove old variant code and add new Genotype predicate for passing filter
Test suite for new Genotype predicate
Test cases for new variant schema updates and test data changes
Update with comments from Frank
Code review feedback & updates
Merge branch 'vcf-work-schema' into vcf-work-remove-old-variant
Command line changes for new variant schema: we modify Vcf2Adam/Adam2Vcf, and remove the implementation of ComputeVariants
Merge pull request #97 from nealsid/vcf-work-schema

New schema, variant context converter changes, and removal of old genoty...
Merge branch 'vcf-work' into vcf-work-remove-old-variant
Code review updates
Cleaning up change documentation.
Merge pull request #107 from fnothaft/cleanup-change-docs

Cleaning up change documentation.
Added the spark.driver.port erasure to SparkFunSuite cleanup.

We've been getting intermittent errors, with respect to Spark being unable to bind to a port,
in the context of repeated unit tests.  This apparently is a known problem, see the thread here:
  http://blog.quantifind.com/posts/spark-unit-test/
and the follow-up from Matei here:
  https://groups.google.com/forum/#!topic/spark-users/MeVzgoJXm8I

The upshot is that we need to clearProperty('spark.driver.port') when we shut down our sparkContext
after a sparkTest.
Merge pull request #104 from genomebridge/tdanford/sparkfunsuite-port

Added the port erasure to SparkFunSuite's cleanup.
New PluginExecutor command

- A plugin class can be defined outside of the Adam jar, but run through
  the normal AdamMain
- An example plugin, the "Take10Plugin" is included in the test
  directory
- Adds a test suite to the cli module, which can reference the items
  available in the core module
- Adds notion of AccessControl to control the records which can be
  accessed
Build Fix & Changes for Frank's comments
Merge pull request #98 from nealsid/vcf-work-remove-old-variant

Vcf work remove old variant
Revert change
Updates for latest strand of comments

- Functional test
- More comments