Fix transform -sort_reads partitioning. Add -coalesce option to transform.

Previously, all unmappped reads when sorting had their referenceId set to
Int.MaxValue. This worked to place unmapped reads at the end of the file
but it also caused all unmapped reads to be placed in a single partition
causing shuffle skew. Unmapped reads are now placed in a range of positions
to distribute them more evenly.
Merge pull request #17 from bigdatagenomics/matt-sortfix

Fix transform -sort_reads partitioning. Add -coalesce option to transform.
Allow the Hadoop version to be specified
Merge pull request #19 from bigdatagenomics/hadoopfix

Allow the Hadoop version to be specified
Added Apache License 2.0 boilerplate to tops of all the GB-copyright files.
Merge pull request #20 from genomebridge/tdanford/licenses

Added Apache License 2.0 boilerplate to tops of all the GB-(c) files
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.
spark-yarn
Revert "spark-yarn"

This reverts commit 38bc7b50eb92518509489fe1d7fc00efaffb6df8.
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