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.