Fixed problem with method Read.getMatePosition returning null value
Updated GCE instance names created by bdutil.
Yet another fix to the matePosition NPE
Merge pull request #24 from elmer-garduno/master

Fixed problem with method Read.getMatePosition returning null value
First take on refactoring VariantsPca.

- Removed VariantCalls (the compact version of a Variant) as it is no longer needed.
- Read the calls ids form the CallSet search API and use them to generate the call indexes.
  - Used the Paginator from genomics.utils to read from the API.
Implemented the mapPartitions summarization.
Added scala doc to public methods on VariantsPca.
Renamed GenomicsConf flags to match the new variant API names.

    --contigs is now --references
    --partitions-per-contig is now --partitions-per-reference
    --max-results is now --page-size
    --reduce-paritions is now --num-reduce-partitions
Added return signature to methods.
Merge pull request #32 from elmer-garduno/spark_pca_refactor

Spark pca refactor
Update docs to show that Spark v1.x is now the default.
Add flag for configurable variantSetId.

Also rename all instances of dataset to variantSet.
Merge pull request #5 from deflaux/spark_pca_refactor

Added variantSetId flag
Merge pull request #34 from elmer-garduno/spark_pca_refactor

Spark pca refactor
Fixed line length.
Merge pull request #35 from elmer-garduno/master

Fixed line length.
Temporarily patched in a hardcoded retry loop.

Instead we should make use of edb16e74dcc19c84a2c1268673edf608d1406f82 per issue #31.
Optionally save output of PCA to configured filesystem.

PCA results are written to stdout.  If an output path is passed in, results will also be written to the configured shared filesystem.

Also removed another cache operation for an RDD that is only used once.
Merge branch 'spark_pca_refactor'
Updates per feedback from @elmer-garduno.
Merge pull request #6 from deflaux/master

Minor changes for runs of PCA on full datasets.