- 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
New Command Line Program to create an interval list from a VCF.
Merge pull request #85 from broadinstitute/gg_vcf_to_interval_list

New Command Line Program to create an interval list from a VCF.
Picard GenotypeConcordance tool
Uses new Genotype Concordance classification scheme
Exports summary and metrics files
fuller unit test coverageg.
modified logic of determine state.
Results of code review:
 - changing logic of use of using VCF Index.
 - consolidating some logic, renaming variables and better comment
 - distinguishing between VariantContext.isMixed and Genotype.isMixed (entirely different).
 - added new Truth/Call State "Missing" and divided "Filter" into vc_filter and gt_filter

Results of code review:
- Improvements to metrics file
- Have GenotypeConcordanceCounts use Histogram
- Improvements to unit tests
Moved CollectHiSeqPfFailMetrics into picard public
Merge pull request #88 from broadinstitute/yf_move_PFFail_to_public

Moved CollectHiSeqPfFailMetrics into picard public
Merge pull request #84 from broadinstitute/gg_genotype_concordance

New Picard Genotype Concordance CLP:
Calculates the concordance between genotype data for two samples in two different VCFs - one being considered the truth (or reference) the other being considered the call.  The concordance is broken into separate results sections for SNPs and indels.  Summary and detailed statistics are reported

Note that for any pair of variants to compare, only the alleles for the samples under interrogation are considered and MNP, Symbolic, and Mixed classes of variants are not included.
Added SAM/BAM/CRAM converter tests. This relies on the jc_cram_changes branch of the htsjdk.
Output CRAM from MarkDuplicates.
Rebase fixes.
SamReader conversion of Picard public.
Deprecation changes.
Added common argument for reference fasta to support CRAM input/output.
Reference fasta should be optional.
Use SamReaderFactory makeDefault with reference sequence whenever possible to allow for CRAM support.