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.