[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-416] Removing 'ADAM' prefix

Includes renames for:
* ADAMFeaturesContext class/object.
* ADAMNucleotideContigFragmentContext/RDDFunctions
* ADAMPileupContext/RDDFunctions and ADAMRODRDDFunctions
* AlignmentRecordContext, AlignmentRecordRDDFunctions
* Variation/GenotypeContext

ADAMContext, ADAMRDDFunctions, ADAMVCFInput/OutputFormats, ADAMMetric*,
and ADAMPredicate were all intentionally left unchanged.

Some method names were also changed, to remove the 'adam' prefix as a
particle within the name.
Merge pull request #418 from tdanford/remove-adam-prefix

[ADAM-416] Removing 'ADAM' prefix
[ADAM-423] Sanitize Avro strings when converting back to SAM.
[ADAM-424] Fix attempts to realign indels when there is no consensus.
[ADAM-425] Skip realignment if no targets are found.
[ADAM-426] Add ability to override indel realigner defaults.
Merge pull request #427 from fnothaft/indel-realigner-errors

Fixes for indel realigner issues