Cleaning up VCF<->ADAM pipeline. Added internal ADAM variant context, that handles the unification of the core variant standard with additional variant/genotype annotations. This variant context also handles the unification of unnested variant and genotype info. In addition to this, the VCF<->ADAM conversion pipeline was upgraded to use Hadoop-BAM/GATK's VariantContext code, to eliminate text parsing. Also, an adam2vcf command was added to do conversion back. A feature to generate variant data from genotype data was suggested and implemented, along with a command.
Merge pull request #13 from bigdatagenomics/new-variant

Cleaning up VCF<->ADAM pipeline
Adding rod functionality: a specialized grouping of pileup data.
Merge pull request #21 from bigdatagenomics/pileup-rods

Adding rod functionality: a specialized grouping of pileup data.
Add a unit test for sorting reads
Merge pull request #22 from bigdatagenomics/matt-sorttest

Add a unit test for sorting reads
Adding support for before, after clauses to SparkFunSuite.

I had a problem, with another branch, where I couldn't access the SparkContext inside a before{}
or after{} block in a SparkFunSuite.  This tries to fix that problem -- and refactors the creation
and destruction of the sparkcontext into separate methods for reuse.

I'm not sure if there's a problem though, with multi-threaded execution of tests?  This seems fragile,
somehow, and could use some comments/review.
Merge pull request #25 from genomebridge/tdanford/sparktest-before

Adding support for before, after clauses to SparkFunSuite.
Add *.log to the .gitignore

So I don't check in my adam.log file, accidentally.
Upping the memory (to 1G) on the scalatest maven plugin.
Generalizing the Projection class.

Added FieldEnumeration and FieldValue class and trait, to help generalize the
values of schemas in enumerations.

Added tests, to ensure that I can use Projection to project the RDDs of two different schemas
(ADAMRecord and ADAMVariant) using the same class but different field enumerations.
Merge pull request #23 from genomebridge/tdanford/general-projection

Generalizing the Projection class
Unmapped read test

- Unmapped reads should be properly handled when loading from sequence dictionary
Handle unmapped reads

- Unmapped reads should not try to go into the sequence dictionary to
  get their information, nor even set their reference id/name
Add unit tests for marking duplicates

Intellij reports the following coverages now:
Class, %         Method, %       Line, %
100% (23/ 23)    94.4% (34/ 36)  94.8% (55/ 58)
Merge pull request #26 from genomebridge/carlyeks/fixUnmappedReadsInSequenceDictionary

Fix unmapped reads in sequence dictionary
Merge pull request #24 from bigdatagenomics/matt-markduptest

Add unit tests for marking duplicates
Fix build warnings

- Make future build warnings fatal, so that we can address them earlier
Merge pull request #28 from genomebridge/carlyeks/buildWarnings

Fix build warnings
Suppress parquet logging in FieldEnumerationSuite