Fix for Adam K's reported bug: we weren't handling reads that were entirely insertions properly in LIBS.  Specifically, the event bases were off-by-one (which was disasterous in Adam's case with a 1bp read).  Added a unit test to cover this case.
Merged bug fix from Stable into Unstable
 number of stashed changes are lurking in here. In order of importance:
 - Fix for M_Trieb's error report on the forum, and addition of integration tests to cover the walker.
 - Addition of StructuralIndel as a class of variation within the VariantContext. These are for variants with a full alt allele that's >150bp in length.
 - Adaptation of the MVLikelihoodRatio to work for a set of trios (takes the max over the trios of the MVLR)
 - InsertSizeDistribution changed to use the new gatk report output (it was previously broken)
 - RetrogeneDiscovery changed to be compatible with the new gatk report
 - A maxIndelSize argument added to SelectVariants
 - ByTranscriptEvaluator rewritten for cleanliness
 - VariantRecalibrator modified to not exclude structural indels from recalibration if the mode is INDEL
 - Documentation added to DepthOfCoverageIntegrationTest (no, don't yell at chartl ;_; )

Also sorry for the long commit history behind this that is the result of fixing merge conflicts. Because this *also* fixes a conflict (from git stash apply), for some reason I can't rebase all of them away. I'm pretty sure some of the commit notes say "this note isn't important because I'm going to rebase it anyway".
Another round of FindBugs fixes. Comparator doesn't implement Serializable.
Another round of FindBugs fixes. Object internally stores a reference to an externally mutable array. Very dangerous.
Another round of FindBugs fixes. Object returns its internal reference to an externally mutable array. Very dangerous.
More merge conflict resolution
Merge branch 'master' of ssh://gsa2.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Merge branch 'master' of ssh://gsa4.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
Enable and adapt HaplotypeScore and MappingQualityZero as active region annotations now that we have per-read likelihoods passed in to annotations
Complete GSA-497: Let Queue write out runInfo on the fly, after each job group finishes running

-- Queue will incrementally now write out its jobReport.txt file whenever jobs finish running (FAIL or DONE)
-- This makes it far easier to track what's going on, or to analyze incrementally performance results coming out of Queue
-- Generally cleaned up the QJobsReporting code, creating a new clean class QJobsReporter that holds all of the information on what to do log and where to put into, which was previously scattered in QCommandLine and QJobReport
GSA-491: Add hidden tag to GATK that propagates to the GATK logs
Update analyzeRunReports.py to handle new GATK tag argument
GATKPerformance over time lives (mark II)

-- Now uses new tagging capabilities so that 2.x runs will tag their logs as GATKPerformanceOverTime
-- Update bamboo runs, reverting back to gsa4 (it's slower but the results are less variable -- you were right david!).
Linear and Quadratic fits for GATKPerformanceOverTime.R
Expand intervals processed for many GATKPerformanceOverTime commands

-- For the high NT tests the total runtime may be too short to really assess nt efficiency vs. start up costs.  Reworked underlying test data and intervals so that most tests run in 10-20 hrs for -nt 1.
run_performance_tests use bsub and gsa

-- Confirmed that running on gsa queue is fine with sufficient iterations (3)
WTF - why is support for whole-read insertions all messed up in LIBS?  I've pushed a temporary patch for now (the right solution should certainly not be implemented in stable; LIBS needs to be better thought out).  Added another unit test.
Merged bug fix from Stable into Unstable
Updating the checkType() function to include the new StructuralIndel variant type. Fixes outstanding broken integration test.