Use original qualities to detect encoding scheme if they are being restored.
Merge pull request #67 from broadinstitute/kt_revert_sam_use_oq_for_detection

Use original qualities to detect encoding scheme if they are being resto...
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
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
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