Add a simple script to be used by Jenkins for testing
Add new pileup and genotype formats for variant calling
Upgrade to Parquet 1.2.4 and fixup jenkins test script
Add all Spark context parameters to commandline
Updated the AdamCommand trait to make non-commandline use easier

This commit separate the commandline processing concerns from the
AdamCommands. This allows command to be used more easily as
part of a library or for testing.
Quick fix to the mpileup command
Add a simple utility class for creation schema projections
Cleanup imports
Use KryoSerializer with embedded Avro objects. New sorting/concat options. SAM support.

o Switch to KryoSerializer with registered handlers for serializing Avro objects
o Add option to sort all reads before writing ADAM/Parquet files
o Add option to concatenate all partitions into a single partition before saving
o Update the bam2adam command to work with both SAM and ADAM files
o Remove the AvroWrapper class as it's no longer needed
o Clean up Parquet commandline options
Merge pull request #7 from massie/matt-s

Use KryoSerializer with embedded Avro objects. New sorting/concat options. SAM support.
Small fix to single partition functionality
Fixed projection object. Was previously causing all projections to contain the empty set.
Merge pull request #8 from fnothaft/adam-projection-fix

Fixed projection object.
Added AdamSparkCommand trait so that AdamCommands can be strung together while using the same Spark context and Hadoop Job config. Updated existing commands to use new trait.
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.
New AdamContext and RichAdamRecord decorators. New RDD methods. Schema fixes.

o Created a new AdamContext decorator for SparkContexts with methods for
  creating new ADAM RDDs from SAM/BAM or ADAM files
o New methods added to RDDs created by ADAM for aggregating pileups, sorting, and
  saving. Makes it easy to compose transformations, e.g. rdd.sort().markDups().save()
o Added new 'RichAdamRecord' decorator for ADAMRecords with useful utility methods
o Fixed a 1-off bug in mateReferencePosition. All offsets are now 0-based.
o Removed the 'end' field from an ADAMRecord and added 'mateReferenceId'