updating the genotype concordance scheme to have called variants that
are filtered be counted as though they are missing
Merge pull request #92 from broadinstitute/nh_update_genotype_concordance_scheme

updating the genotype concordance scheme to have called variants that
Picard release 1.123

Picard release 1.123
Intermediate checking of hard filtering code.
Second round of changes to implement a VCF hard filtering program.
Added unit tests and fixed the need for a VCF index.
Made constructor public in public class!
Added a QD filter and plumbed it into FilterVcf