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.
This makes a fundamental change to how we run Picard.  We now have a
single JAR (command line program), rather than multiple JAR (one per
tool). In this brave new world, the single command line program is given
the the command line program name (ex. SamView) to specify which tool to
run.  We also provide a convenient summary of all of the tools
available.

For the developers, we add a facility to add new command line programs
to the single JAR, by extending the PicardCommandLine and adding the
package name(s) for us to search for classes that extend
CommandLineProgram.  The usage is now put in
CommandLineProgramProperties, where we can also specify short usages
(for the summary help message), program versions, and program groups.
The latter is useful for grouping tools that operate on common filetypes
or have similar function (ex. SAM/BAM).

We made a number of new tools public, coming from our internal toolset.
These include: BaitDesigner, CalculateReadGroupChecksum, CheckTerminatorBlock,
CollectIlluminaBasecallingMetrics, CollectIlluminaLaneMetrics,
CollectJumpingLibraryMetrics, CollectOxoGMetrics,
CollectQualityYieldMetrics, CollectRrbsMetrics, GatherVcfs,
LiftOverIntervalList, ScatterIntervalsByNs, and SplitSamByLibrary.
These may prove useful, or not.

Enjoy!