Changing to AvroParquetOutputFormat.
Added logging to partitioner for diagnosing skew issues.
Add Beacon's AlleleCount

This is the preprocessing step of AMPLab Beacon. It parses an ADAM
variant and creates a text file with counts of allele frequencies.
Merge pull request #301 from genomebridge/beacon-allele-count

Add Beacon's AlleleCount
Adding intersection to reference region class.