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.
Upgrade from Hadoop-BAM 5.3 to 6.0

This commit removes the checked in local maven repo and replaces
it with a remote private one. This helps to avoid checking large
files into this git repo.

In order to reduce dependencies, the BCF/VCF code has been removed
from Hadoop-BAM. I've talked with the Hadoop-BAM team about how
to publish maven artifacts that are compatible with all versions of
Hadoop. In the future, we will remove the Hadoop-BAM source
altogether and simply depend on a published artifact.