Modified reads2ref code to fix performance issue. 

There was an issue in the reads2ref aggregation code that would cause out of memory errors when doing a groupBy. I changed this code to set the partition number roughly off of the coverage. I believe this is preferable, but I have provided mechanisms for overriding this if one does not want to increase their partition number, or if one wants to otherwise set the partitioning.

Also, I broke the code up to add a reads2pileups RDD function.