Brought all of ReduceReads to fastutils

-- Added unit tests to ReduceReads name compression
-- Updated reduce reads walker for unit testing

GSATDG-83
Addressing Eric's comments

-- added @param docs to the new variables
-- made all variables final
-- switched to string builder instead of String for performance.

GSATDG-83
Refactored PairHMM.initialize to first take haplotype max length and then the read max length so that it is consistent with other PairHMM methods.
Fixed the intermittent PairHMM unit test failure.

The issue here is that the OptimizedLikelihoodTestProvider uses the same basic underlying class as the
BasicLikelihoodTestProvider and we were using the BasicTestProvider functionality to pull out tests of
that class; so if the optimized tests were run first we were unintentionally running those same tests
again with the basic ones (but expecting different results).
AGBT analysis scripts

-- Simple scripts to realign BAMs around indels and run HC scatter gathered
-- AGBT analysis R script
Merge pull request #60 from broadinstitute/mc_fastutil_GSATDG-83

Brought all of ReduceReads to fastutils
Merge pull request #63 from broadinstitute/eb_fix_pairhmm_unittest_GSA-776

Eb fix pairhmm unittest gsa 776
Shell script to release GATK nightly builds

-publishes GATK jar + accompanying GATKDocs archive to a new
 nightly build directory

-nightly builds are versioned by date rather than tag
Merge pull request #69 from broadinstitute/dr_nightly_build_script_GSATDG-78

Shell script to release GATK nightly builds
Nightly build script improvements

-Include the word "nightly" in the version

-Add a ".tar.bz2" extension to the symlinks for the current build
Merge pull request #70 from broadinstitute/dr_nightly_build_script_adjustments

Nightly build script improvements
Merged bug fix from Stable into Unstable
Merged bug fix from Stable into Unstable
Merged bug fix from Stable into Unstable
GATKPerformanceOverTime now includes a mode to comparing HC & UG performance

-- Compares HC and UG performance on single deep genomes and 140 WEx bams over small intervals, as well as deep WGS reduced data and 1000G 4x data
-- Added mode to GATKPerformanceOverTime to include lots of versions, so we can make beautiful graphs of the cost of tools over many versions as well
-- Marginally better plots for multiple iterations in GATKPeformanceOverTime.R
Merge pull request #72 from broadinstitute/md_profile_hc_vs_ug_GSA-749

GATKPerformanceOverTime now includes a mode to compare HC & UG performance
Eliminate 7-element arrays in BaseCounts and BaseAndQualsCount and replace with in-line primitive attributes.  This is ugly but reduces heap overhead, and changes are localized.  When used in conjunction with Mauricio's FastUtil changes it saves and additional 9% or so of execution time.
Merge pull request #68 from broadinstitute/aw_reduce_reads_perf

Eliminate 7-element arrays in BaseCounts and BaseAndQualsCount and repla...
Replace uses of NestedHashMap with NestedIntegerArray.

 * Removed from codebase NestedHashMap since it is unused and untested.
 * Integration tests change because the BQSR CSV is now sorted automatically.
 * Resolves GSA-732
Merge pull request #64 from broadinstitute/md_agbt