Moved SortVCF to public
Generalized MergeVcfTest and added a unit test specific to SortVCF

MergeVcfTest had many of the input-validation tests I wanted to perform on SortVCF as well.

Did some minor cleanup to SortVCF as well.
SortVcf changes to address code review
Merge pull request #68 from broadinstitute/bt_sort_vcf_enhancement_PFB-981

Adding enhanced SortVcfs CLP
Fix so BAMRecordCodec will recognize when qual array has been changed.
Merge pull request #70 from broadinstitute/kt_fix_qual_rewrite_for_bams

Fix so BAMRecordCodec will recognize when qual array has been changed.
- Added a static function to PedFile that allows the creation of a pedFile object from a Map<String,Sex>.
- Added a test
Merge pull request #75 from broadinstitute/yf_ped_file_update

Added a static function to PedFile
updating location of HTSJDK's version property file
Merge pull request #74 from broadinstitute/nh_htsjdk_version_file_update

updating location of HTSJDK's version property file
Picard version 1.121
Picard GenotypeConcordance tool
Additional unit tests.
renaming inputs to describe truth and call samples
adding in docs for TS and CS
reversing concordance truth vs. call ordering in the output
Added optimization to only use the VCF index if scanning < 25% of the file.
Changed detailed output format.  Updated expected test output files accordingly.
Added calculation of Specificity.
Added Results of code review.
1) Refactored to move reusable classes to separate files
2) Added filtering by variant type (only include SNP/indel in concordance).
Converted to generate metrics files
updated unit tests to handle new output.
Added False positives / megabase as a summary metric
Add code to flag mismatching alleles on Homvar/Homvar and het/het comparisons.  Unit tests for same.
Allow for disagreeing ref alleles (for indel indel comparisons)
adding a first pass at providing an API to the Genotype Concordance
Table and Scheme.
more updates to determine states, and adding filtering columns/rows
Changed to use GenotypeConcordanceCounts
Removed old GenotypeConcordance methodology.  Converted most unit tests.
Handle mismatched ref alleles.  Deal with different ordering of alleles between truth and call