Modifying interleaved fastq format to be hadoop version independent.
Merge pull request #289 from fnothaft/ifq-debug

Modifying interleaved fastq format to be hadoop version independent.
Cleaning up scaladoc generation warnings.
Add aggregation and display of metrics obtained from Spark

This change adds an new command-line option called "print_metrics" which causes a listener to be registered with Spark, which accumulates metrics when each task and stage end. When a command is complete the metrics are logged to stdout.
Running ./scripts/format-source on files checked-in by previous commit (498d8377651d21e86ff642071e6c9b1d585db4cc)
Merge pull request #292 from fnothaft/clean-scaladoc

Cleaning up scaladoc generation warnings.
Logging metrics to the Spark logger instead of stdout
Set a larger output buffer for printing metrics
Changes based on review of PR 292 (Add aggregation and display of metrics obtained from Spark)
Removed btc ascii table library and added class to render ascii tables
Fix broken link to ADAM specification for storing reads.
Merge pull request #295 from roryk/master

Fix broken link to ADAM specification for storing reads.
Merge pull request #293 from nfergu/spark-metrics

Add aggregation and display of metrics obtained from Spark
Remove reference to unused Maven repository
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.
Added the TrackedLayout class.