Resurrect VCF conversion code
Update & add test cases to PR
CR feedback
Fix build break
Add back CLI code from our variant branch, unit tests, as well as adam2vcf code
Add concordance class and rich AdamGenotype class, and Genotype RDD functions class
Remove an extra comment and add a TODO to unify genome locations around ADAM Contig
Code review feedback
Merge pull request #147 from nealsid/vcf-work-vcf-conversion

Resurrect VCF conversion code
Merge branch 'vcf-work' into vcf-work-adam2vcf-and-cli
Merge branch 'vcf-work' into vcf-work-concordance-and-genotype
Merge pull request #150 from nealsid/vcf-work-adam2vcf-and-cli

Remaining variant changes for adam2vcf, unit tests, and CLI modifications
Merge pull request #151 from nealsid/vcf-work-concordance-and-genotype

Vcf work concordance and genotype
Merge remote-tracking branch 'origin/pr/157'

Conflicts:
	adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/rdd/AdamContext.scala
Remove ADAMVariantAnnotations import
Added a region-join implementation.

Fixes ISSUE #83.
- This allows for joining different types which are aligned to different
  ReferenceRegions
- A record will appear in multiple different places when it overlaps
  multiple different regions

For testing purposes, we've also added a 'cartesian join' implementation, which
operates by using the cartesian product operation on RDDs, followed by a filter.
This should be logically equivalent to the region join implementation here, but
is probably slow enough that we would only use it for testing in real-life situations.

Added SequenceDictionary.containsRefId to support the regionJoin operation.

An example of using the regionJoin method is presented in the new CLI command,
CalculateDepth.  CalculateDepth (accessible as the command 'depth' through AdamMain)
takes two arguments, an ADAMRecord file and a VCF (or equivalent) file, and calculates
the number of reads (the 'depth') from the ADAMRecord file which overlap each of the
variants given by the VCF.  It then reports, on standard out, the location and name
of each variant along with the calculated depth.

Adding comments.

Renamed some methods, some classes, and added extensive comments.
Merge pull request #117 from genomebridge/regionJoin

Add a "range join" method.
Added switches to spark context creation code to allow buffer size increase and increased logging for profiling.
Merge pull request #161 from fnothaft/context-debug

Added switches to spark context creation code
Add util.BuildInformation and buildinfo command

This is a first attempt at #41.

- adam-core: Add git-commit plugin to POM file. The file is generated
is `adam-core/src/main/resources/git.properties` and the info is
available in the object
`edu.berkeley.cs.amplab.adam.core.util.BuildInformation`.
- adam-cli: Add the command `buildinfo`.