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
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.