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