Merge pull request #292 from broadinstitute/vrr_analyzeCovariates

Added the AnalyzeCovariates tool to generate BQSR quality assessment plots.
Fix public / protected dependency
Merge pull request #296 from broadinstitute/md_pubprotfix

Fix public / protected dependency
Remove debug print statement
Better GATK version and command line output

-- Previous version emitted command lines that look like:

##HaplotypeCaller="analysis_type=HaplotypeCaller input_file=[private/testdata/reduced.readNotFullySpanningDeletion.bam] ..."

the new version provides additional information on when the GATK was run and the GATK version in a nicer format:

 ##GATKCommandLine=<ID=HaplotypeCaller,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:09:01 EDT 2013",Epoch=1371740941197,CommandLineOptions="analysis_type=HaplotypeCaller input_file=[private/testdata/reduced.readNotFullySpanningDeletion.bam] read_buffer_size=null phone_home=AWS ...">

 -- Additionally, the command line options are emitted sequentially in the file, so you can see a running record of how a VCF was produced, such as this example from the integration test:

 ##GATKCommandLine=<ID=HaplotypeCaller,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:09:01 EDT 2013",Epoch=1371740941197,CommandLineOptions="lots of stuff">
 ##GATKCommandLine=<ID=SelectVariants,Version=2.5-206-gbc7be2b,Date="Thu Jun 20 11:16:23 EDT 2013",Epoch=1371741383277,CommandLineOptions="lots of stuff">

 -- Removed the ProtectedEngineFeaturesIntegrationTest
 -- Actual unit tests for these features!
Merge pull request #297 from broadinstitute/md_vcfversion2

Better GATK version and command line output
Merge remote-tracking branch 'unstable/master'
Update README file for the 2.6 release
Update source release script in attempt to work around intermittent github issues

Github was intermittently rejecting large pushes that were in fact
fast-forward updates as being non-fast-forward. Try to prevent this
by ensuring that all refs are up-to-date and properly checked out
after branch filtering and before doing a source release.
Error out when NCT and BAMOUT are used with the HaplotypeCaller

-- Currently we don't support writing a BAM file from the haplotype caller when nct is enabled.  Check in initialize if this is the case, and throw a UserException
VariantRecalibrator bugfix for bad log10sumlog10 values

-- The VR, when the model is bad, may evaluate log10sumlog10 where some of the values in the vector are NaN. This case is now trapped in VR and handled as previously -- indicating that the model has failed and evaluation continues.
Experimental LikelihoodRankSum annotation

-- Added experimental LikelihoodRankSum, which required slightly more detailed access to the information managed by the base class, so added an overloaded getElementForRead also provides access to the MostLikelyAllele class
-- Added base class default implementation of getElementForPileupElement() which returns null, indicating that the pileup version isn't supported.
-- Added @Override to many of the RankSum classes for safety's sake

-- Updates to GeneralCallingPipeline: annotate sites with dbSNP IDs,
-- R script to assess the value of annotations for VQSR
Another fix for the Indel Realigner that arises because of secondary alignments.

This time we don't accidentally drop reads (phew), but this bug does cause us not to
update the alignment start of the mate.  Fixed and added unit test to cover it.
Added the pertinent DocumentedGATKFeature annotation ot AnalyzeCovariates
Merge pull request #299 from broadinstitute/eb_mate_fixer_confused_by_nonprimary_alignment

Another fix for the Indel Realigner that arises because of secondary alignments.
Merge pull request #300 from broadinstitute/mc_move_qualify_intervals_to_protected

Few bug fixes to this tool now that it is in protected
quick fixes to the scala script

   * Increase the memory limit for HTSLIB - Bam shuffling just eats up a ton of memory.
   * Concurrent HTSLIB processes need unique temp files the bam shuffling step was messing up with the temporary files and failing without returning zero. Fixed it by giving a unique name to each process.
Merge pull request #302 from broadinstitute/mc_processing_pipeline2

quick updates to the techdev processing pipeline scala script
Merged bug fix from Stable into Unstable
Fixing the 'header is negative' problem in Reduce Reads... again.

Previous fixes and tests only covered trailing soft-clips.  Now that up front
hard-clipping is working properly though, we were failing on those in the tool.

Added a patch for this as well as a separate test independent of the soft-clips
to make sure that it's working properly.