Added output writer format for Hadoop-BAM that is compatible with Spark writer format.
Added comment to explain/justify code smell.
Merge pull request #9 from fnothaft/adam-bam-writer

Added output writer format for Hadoop-BAM that is compatible with Spark
Split reads2ref into read to pileup and aggregation operation.

Created new command to handle aggregation. Aggregation can also be
done inside reads2ref command with -compress switch.  Additionally,
fixed bug with base quality.