Picard GenotypeConcordance tool
Uses new Genotype Concordance classification scheme
Exports summary and metrics files
fuller unit test coverageg.
modified logic of determine state.
Results of code review:
 - changing logic of use of using VCF Index.
 - consolidating some logic, renaming variables and better comment
 - distinguishing between VariantContext.isMixed and Genotype.isMixed (entirely different).
 - added new Truth/Call State "Missing" and divided "Filter" into vc_filter and gt_filter

Results of code review:
- Improvements to metrics file
- Have GenotypeConcordanceCounts use Histogram
- Improvements to unit tests
Merge pull request #84 from broadinstitute/gg_genotype_concordance

New Picard Genotype Concordance CLP:
Calculates the concordance between genotype data for two samples in two different VCFs - one being considered the truth (or reference) the other being considered the call.  The concordance is broken into separate results sections for SNPs and indels.  Summary and detailed statistics are reported

Note that for any pair of variants to compare, only the alleles for the samples under interrogation are considered and MNP, Symbolic, and Mixed classes of variants are not included.