Added switches to spark context creation code

Adds the following switches to the spark context creation code:

* A switch to allow for configuring the size of the Spark Kryo buffer. This is necessary for indel realignment on larger datasets.
* A switch to add a logger that prints debug text after every stage. This debug text contains information about data movement inside of the command that is being run, and is useful for performance analysis/profiling.

This addresses #149.