Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Getting back null values from the tables is perfectly reasonable if those covariates don't appear in your table. Need to handle them gracefully.
GenomeLocs are already comparable, so I'm removing the less complete GenomeLocComparator class and updating ReduceReads and CompressionStash to use built-in comparator
Refactoring the SimpleGenomeLoc into the now public utility UnvalidatingGenomeLoc and the RR-specific FinishedGenomeLoc.
Moved the merging utility methods into GenomeLoc and moved the unit tests around accordingly.
Resolving merge conflicts
UnitTesting example for copying

-- Example combinatorial unit tests, plus unit tests that create reads and bam files, pileups, variant context (from scratch and from a file), and genome locs
The Empirical quality column in the recalibration report can't be compared in the BQSRGatherer because the value is calculated using the Bayesian estimate with different priors. This value should never be used from a recalibration report anyway except during plotting.
Remove FindContaminatingReadGroups walker and associated untested utils.NamedTable code
Move BaseUtils back to the GATK by request, along with associated utility methods
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
Adding unit tests for hierarchicalBayesianQualityEstimate function
Updating BQSR integration test md5s to reflect the updates to the hierarchicalBayesianQualityEstimate function
Move additional VariantContext utility methods back to the GATK

Thanks to Eric for his feedback
Breaking up my massive commits into smaller pieces that I can successfully merge and digest. This one enables downsampling in the HaplotypeCaller (by lowering the default dcov to 20) and removes my long-standing, temporary region-based downsampling.
Encrypt GATK AWS keys using the GATK private key, and decrypt as needed as a resource when uploading to AWS logs

-- Has the overall effect that the GATK user AWS keys are no longer visible in the gatk source as plain text.  This will stop AWS from emailing me (they crawl the web looking for keys)
-- Added utility EncryptAWSKeys that takes as command line arguments the GATK user AWS access and secret keys, encrypts them with the GATK private key, and writes out the resulting file to resources in phonehome.
-- GATKRunReport now decrypts as needed these keys using the GATK public key as resources in the GATK bundle
-- Refactored the essential function of Resource (reading the resource) from IOUtils into the class itself.  Now how to get the data in the resouce is straightforward
-- Refactored md5 calculation code from a byte[] into Utils.  Added unit tests
-- Committing the encrypted AWS keys
-- #resolves https://jira.broadinstitute.org/browse/GSA-730
Use base List and Map types in the HaplotypeCaller when possible.
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
few changes in the generalCallingPipeline
Merge branch 'master' of github.com:broadinstitute/gsa-unstable
More aggressive checking of AWS key quality upon startup in the GATK