Spark pca example

Hi @cassiedoll, @deflaux I added code for computing the genome wide PCA, please have a look and let me know what you think.

Thanks, 

@elmer-garduno, that makes sense and thank you for the added changes.  Yes, I agree that sim-matrix will be useful for other analysis.

The WordCount approach is nice, but how will you search these cache files or consolidate results from multiple ones later on?  Currently it is being performed by accessing them one at a time, which is a perfect start but most likely these will be many and results across many will be helpful to be integrated for comprehensive analysis.