fix refname comment
Merge pull request #283 from hammerlab/refname-comment

Fix reference name comment
Removing ADAM format directory, and updating avro data file path and pom.xmls for bdg-formats move.
Merge pull request #280 from fnothaft/move-to-bdgformats

Move to bdg-formats
Cleaning up build warnings.
Merge pull request #284 from fnothaft/clean-warnings

Cleaning up build warnings.
Refactoring read groups to increase the amount of data stored.
Merge pull request #285 from fnothaft/sample-to-converter

Refactoring read groups to increase the amount of data stored.
Removing some debug printout that was left in...
Adding further exclusions to clean up issues that make it difficult to run downstream jobs with hadoop versions other than 2.2
Merge pull request #287 from fnothaft/hadoop-dependencies

Cleaning hadoop dependencies
Merge pull request #286 from fnothaft/remove-debug-printout

Removing some debug printout that was left in.
Add ADAMFeature to Kryo registrator
Merge pull request #288 from laserson/adam-feature-kryo

Add ADAMFeature to Kryo registrator
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.