Load dbSpec into string before parsing it as JSON

This is to make the causes of errors more obvious; if there is an error parsing the json string the entire received message is included in the error message
Make sure to follow HTTP redirects when loading dbSpec
Update pom versions to mark the start of GATK 3.2 development
Temporarily disable GATKRunReportUnitTest in unstable while maven issues are worked out

This test passes when run individually, as part of the commit tests, or as
part of the package tests. However, when running the unit tests in isolation
it causes maven/surefire to throw a NoSuchElementException.

This is clearly a maven/surefire bug or configuration issue. I will re-enable
this test on a branch as Khalid and I try to work through it.
Merged bug fix from Stable into Unstable
Re-enable GATKRunReportUnitTest

This test is not, as I had initially thought, the cause of the
maven errors. Our master branch is failing intermittently
regardless of whether this test is enabled or disabled.

This reverts commit 45fc9ff515eec8d676b64a04fb34fb357492ff84.
Small argument docs fix in AssessNA12878.
Fix typo in UtilsUnitTest data provider name

This is currently my leading suspect for the cause of the
intermittent NoSuchElementException errors on master, since
the maven surefire plugin seems unable to handle errors in
TestNG DataProviders without blowing up.
Merge pull request #568 from broadinstitute/dr_fix_UtilsUnitTest

Fix typo in UtilsUnitTest data provider name
Merge pull request #566 from jsilter/master

Improvements to na12878kb
Reduce runtime of very long integration test
Merge pull request #569 from broadinstitute/vrr_speedup_integration_test

Reduce runtime of very long integration test
Merge pull request #570 from broadinstitute/rp_assessNA12878_arg_docs_fix

Small argument docs fix in AssessNA12878.
Fixing the reference base in one of the manual review files.
Merge pull request #571 from broadinstitute/rp_fix_manual_reviews

Fixing the reference base in one of the manual review files.
Forgot to change the padding ref base as well.
Merge pull request #572 from broadinstitute/rp_fix_manual_reviews_fix

Forgot to change the padding ref base as well.
Have CombineVariants throw a UserError when trying to combine GVCFs from the HaplotypeCaller.

Was previously throwing an IllegalArgumentException (in the wrong place in the code).
Error message tells users to use CombineGVCFs.
Enable CombineGVCFs to process gVCFs that were created with basepair resolution.
Several improvements to GenotypeGVCFs: --includeNonVariantSites now actually works and we propagate AD to hom ref samples