RDD functions for new variant schema
New test suites for RichADAMVariant, AdamContext, AdamVariationContext, ADAMVariantContextRDDFunctions, FieldEnumerationSuite
Remove out-of-date reference to CompareAdam
Merge branch 'master' of https://github.com/bigdatagenomics/adam into vcf-work-rdd-master-merge

Conflicts:
	adam-cli/src/main/scala/edu/berkeley/cs/amplab/adam/cli/Adam2Vcf.scala
	adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/converters/VariantContextConverter.scala
	adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/models/ADAMVariantContext.scala
	adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/rdd/AdamContext.scala
	adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/rdd/AdamRDDFunctions.scala
	adam-core/src/test/scala/edu/berkeley/cs/amplab/adam/converters/VariantContextConverterSuite.scala
	adam-core/src/test/scala/edu/berkeley/cs/amplab/adam/models/ADAMVariantContextSuite.scala
	adam-format/src/main/resources/avro/adam.avdl
Fix bad merge that missed ADAMNucleotide* types & classes
Code review changes
Fix tests & build of adam-core
Merge branch 'vcf-work-rdd' into vcf-work-rdd-master-merge
Merge pull request #114 from nealsid/vcf-work-rdd

Changes to RDD utility files for new variant schema
Merge branch 'vcf-work' into vcf-work-rdd-master-merge
Text & code fixes from merge
Update README.md

To improve the experience for users trying to build ADAM from source, I think it's worth explicitly adding the command to up the PermGen size and to turn off running tests, which should reduce the number of emails to the mailing list about failing builds and allow the new user to get moving with the jar file sooner rather than later.

Feel free to discard if you think either change does more harm than good.
Merge pull request #139 from hammer/patch-1

Update README.md
Update README.md

Change the remote URL to use HTTPS rather than SSH, as [GitHub recommends for users behind a firewall or proxy](https://help.github.com/articles/which-remote-url-should-i-use).
Merge pull request #140 from hammer/patch-2

Update README.md
Changing package declaration to match test file location and removing unused imports and unnecessary semicolons.
Merge pull request #143 from hammerlab/ifq-test-cleanup

Changing package declaration to match test file location and removing unused imports and unnecessary semicolons.
Fixed a couple bugs in the test cases (UTF8->Scala string conversion, and left outer join bug)
Update code to use integers for reference/contig ids
Merge pull request #124 from nealsid/vcf-work-rdd-master-merge

Vcf work rdd master merge
Merge branch 'master' of https://github.com/bigdatagenomics/adam into vcf-work-master-merge