Added CLI options for the SearchReadsExample using scallop.
Updated README.md to document the new flag values.
Updated README file to the new configuration options
Merge pull request #3 from elmer-garduno/add_scallop_options

Added runtime configuration flags
Added instructions to run spark-examples on GCE.

Updated the README with instructions on how to run the examples on GCE.
Updated SearchReadsExample1 to print the results on the local console.

Also did a small refactoring to create the spark context from the configuration.
Fixed README style.
Merge pull request #4 from elmer-garduno/docs_run_on_gcloud

Added instructions to run spark-examples on GCE.
Merge pull request #1 from deflaux/master

An initial stab at an RDD for Variant Store.
Merge remote-tracking branch 'upstream/master'
Merge pull request #5 from elmer-garduno/master

Merge pull request #1 from deflaux/master
Merge remote-tracking branch 'upstream/master'
Fix minor typo in README
Updated the variant creation methods to be type safe.

By building directly from the API methods when available.
Also updated null arguments to Option.
Merge pull request #6 from elmer-garduno/serialize_java_api_objects

Serialize java api objects
Consolidated transforming from the Java API objects to the serializable version on a ReadBuilder object.

This adds type safety as the values are no longer transformed into a Map, the class constructor is invoked directly using the appropriate types.
Merge pull request #7 from elmer-garduno/serialize_java_api_objects

Updated ReadsIterator to the ReadBuilding pattern.
Merge pull request #1 from elmer-garduno/master

update from upstream