Supplemental alignments are now considered when fixing mate information
in FixMateInformation and RevertOriginalBaseQualitiesAndAddMateCigar.
Merge pull request #64 from broadinstitute/nh_really_fix_supplementals

Supplemental alignments are now considered when fixing mate information
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)