[ADAM-405] Add FASTQ output.
Merge pull request #408 from fnothaft/fastq-output

[ADAM-405] Add FASTQ output.
[ADAM-411] Updated usage aliases in README. Fixes #411.
Merge pull request #412 from laserson/update-alias

[ADAM-411] Updated usage aliases in README. Fixes #411.
Fix error in `adam-local` alias
Update README.md
Merge pull request #415 from laserson/patch-2

Update README.md to reflect Spark 1.1
Merge pull request #414 from laserson/patch-1

Fix error in `adam-local` alias
Adding 'testFile' to SparkFunSuite

Makes it easier to load files from teh classpath.
Updating the bdg-formats dependency to 0.3.1
[ADAM-381] Fixes Pileup usage in bdg-formats 0.3.1

Removing the usage of now-deleted fields in the new Pileup schema.
[ADAM-327] Adding Gene, Transcript and Exon models
Merge pull request #404 from tdanford/gene-models

[ADAM-327] Adding gene, transcript, and exon models.
[ADAM-401] Adding read error correction.