Update pom versions to mark the start of GATK 3.3 development
Added -gtType argument to AssessNA12878 to stratify assessment based on true genotype call in NA12878 (or input call if the former is not in KB).

Story:

  https://www.pivotaltracker.com/story/show/75028590

Changes:

  Added the possibility of indicating the genotype type to consider (with argument [-gtType TYPE]*, where TYPE is HET, HOM_REF or HOM_VAR)
  Removed conditional Het evaluation based on input ploidy; now you need to use -gtType explictly.

Tests:

  Added integration tests to check on new argument (-gtType) behaviour in AssessNA12878KnowledgeBaseTest
Updated na12878kb-utils with classes from old ant StingUtils.jar.
Fixed package names post picard/htsjdk renaming.
Merge pull request #687 from broadinstitute/vrr_omniploidy_assesment_na12878

Further changes to AssessNA12878 for evaluating Omniploidy
The copy constructor for a GATKSAMRecord (used for testing only) should use the actual read's contig index, not its mate's.
Merge pull request #689 from broadinstitute/eb_fix_samrecord_test_constructor

The copy constructor for a GATKSAMRecord (used for testing only) should ...
Add diploid only support message to HaplotypeCaller

Story:

  https://www.pivotaltracker.com/story/show/73440292

Changes:

  - Just add the conditional in HaplotypeCaller#initialize

Testing:

  - Nothing added, checked locally, trivial change that would eventually be removed anyway.
Merge pull request #690 from broadinstitute/vrr_fix_non_diploid_unsupproted_message_in_haplotype_caller

Add diploid only support message to HaplotypeCaller
Update GATK to work with latest htsjdk
ValidationStringency was moved from htsjdk.samtools.SAMFileReader to htsjdk.samtools
samtools find BAM index file method was also moved (and made public!)
Merge pull request #691 from broadinstitute/ldg_update_htsjdk

Update GATK to work with latest htsjdk
Fixing typos in AnalyzeCovariates
Merge pull request #692 from broadinstitute/rp_typo_analyze_covariates

Fixing typos in AnalyzeCovariates
Allow SOR to be calculated from HC
Refactor StrandBiasTest classes
Documentation fix (closed HTML tag)
Merge pull request #695 from broadinstitute/pd_genotype_concordance_doc

Documentation fix (closed HTML tag)
Improved detection of missing argument values
 In particular, it was possible to specify arguments for Files or Compound types without values
 Added a special "none" value for annotations, since a bare "-A" is no longer allowed
 Delivers PT 71792842 and 59360374
Fix sample sort order bug in DepthOfCoverage
 Rare bug triggered by hash collision between sample names
 PT 66183936
Merge pull request #694 from broadinstitute/pd_check_missing_arg_values

Improved detection of missing argument values
Merge pull request #696 from broadinstitute/pd_DoC_sorting

Fix sample sort order bug in DepthOfCoverage
Merge pull request #693 from broadinstitute/ldg_SORfromHC

Allow SOR to be calculated from HC