Rewrite of MarkDuplicates which seems to improve performance
Moved methods around to make diffing with the previous version easier
Modified loops in markReadsInBucket to use collection.foreach
[ADAM-387] fix some deprecation warnings

- move from deprecated SAMFileReader to SamReader
- move off of a deprecated scalatest method
Merge pull request #387 from ryan-williams/deprecations
Added "read pairs that cross chromosomes" to MarkDuplicatesSuite
Merge pull request #380 from nfergu/markduplicateschanges

Rewrite of MarkDuplicates which seems to improve performance
[ADAM-237] Migrate to Chill serialization libraries.
Merge pull request #391 from fnothaft/chill-serializers

[ADAM-237] Migrate to Chill serialization libraries.
[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.