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
updating how _includes/command-line-usage.html is generated on the docs
page: moving from virtual include to markdown include

see: https://github.com/broadinstitute/picard/issues/77
New CLP to update the sequence dictionary for one with VCF with that from another.
Moved Yossi's SAMSequenceDictionaryExtractor over to htsjdk from picard
Merged same into UpdateVcfSequenceDictionary code.
Adding a new tool with which to mark duplicates:
MarkDuplicatesWithMateCigar.

This tool can replace MarkDuplicates if the input SAM/BAM has Mate CIGAR (MC) optional tags
pre-computed (see the tools RevertOriginalBaseQualitiesAndAddMateCigar and
FixMateInformation).  This allows the new tool to perform a streaming duplicate
marking routine (i.e. a single-pass).  This tool cannot be used with
alignments that have large gaps or reference skips, which happens
frequently in RNA-seq data.

There were many refactors of the old MarkDuplicates and
MarkDuplicatesWithMateCigar, since the share common code.
EstimateLibraryComplexity was caught up in this too.

Many, many, many unit tests were added to were added to prove
equivalency of MarkDuplicatesWithMateCigar to MarkDuplicates.  This also
exposed a few one in a million corner cases in MarkDuplicates both in
duplicate marking as well as optical duplicate detection.  This results
in MarkDuplicates needing to write slightly larger temporary files when
running.  SamFileTester was also improved to handle the various test
cases for duplicate marking testing.
Merge pull request #79 from broadinstitute/bt_mark_duplicates

Adding a new tool with which to mark duplicates:
Merge pull request #71 from broadinstitute/gg_UpdateVcfDictionary

A new CLP to update the sequence dictionary of a VCF from another file (SAM, BAM, VCF, dictionary, interval_list, fasta, etc).
Merge pull request #78 from broadinstitute/nh_cmd_line_usage_docs_fix

updating how _includes/command-line-usage.html is generated on the docs
changing link to IntervalList.java documentation
Merge pull request #82 from broadinstitute/nh_testdata_links_to_github

changing link to IntervalList.java documentation
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)
Switching GenotypeConcordance tool over to a more flexible framework for determine state