modified logic of determine state.
Results of code review - changing logic of use of using VCF Index.
Results of code review - Consolidating some logic, renaming variables and better comment
updating default scheme: squash me

Conflicts:
	src/java/picard/vcf/GenotypeConcordanceScheme.java
Results of code review - Distinguishing between VariantContext.isMixed and Genotype.isMixed (entirely different).
Merge branch 'gg_genotype_concordance' of github.com:broadinstitute/picard into gg_genotype_concordance_v2

Conflicts:
	src/java/picard/vcf/GenotypeConcordance.java