[ADAM-393] Adds knobs to the SparkContext creation process in SparkFunSuite.
Merge pull request #394 from fnothaft/fun-suite

[ADAM-393] Adds knobs to SparkContext creation in SparkFunSuite
[ADAM-388][ADAM-398] Sets Kryo serialization with --conf args

Fixes #388
Fixes #398: Updated `jenkins-test` script to dnload Spark 1.1
Merge pull request #396 from laserson/conf-args

[ADAM-388] Sets Kryo serialization with --conf args
[ADAM-399] Fix link to schemas.
Merge pull request #400 from fnothaft/fix-formats-link

[ADAM-399] Fix link to schemas.
[ADAM-384] Adds import from FASTQ.
Merge pull request #385 from fnothaft/fastq-input

[ADAM-384] Adds import from FASTQ.
[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