New Command Line Program to create an interval list from a VCF.
Merge pull request #85 from broadinstitute/gg_vcf_to_interval_list

New Command Line Program to create an interval list from a VCF.
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