[RNAdam-38] Fix broken build due to upstream changes.
[RNAdam-39] Removing local Gene model stubs
Merge pull request #40 from fnothaft/downstream-updates

Upgrading to downstream updates in ADAM
Implemented the mapKmersToClasses method in Quantify.scala
Addresses RNAdam Issue Number 31
Merge pull request #37 from niranjan93/NK_mapKmersToClasses

Implemented the mapKmersToClasses method in Quantify.scala
[RNAdam-34] Added joinTranscripts in Quantify
Merge pull request #41 from ananth-pallaseni/joinTranscrip

[RNAdam-34] Added joinTranscripts in Quantify
[RNAdam-42] Remove sequence dictionary from region join.
Merge pull request #43 from fnothaft/fix-rj-build

[RNAdam-42] Remove sequence dictionary from region join
[RNAdam-32] Added EM initialization code. Addresses RNAdam Issue Number 32.
Merge pull request #44 from niranjan93/NK_initializeEM

[RNAdam-32] Added EM initialization code. Addresses RNAdam Issue Number 32.
[RNAdam-45] Collect transcript lengths before running EM.
Cleaned up Quantify/QuantificationTestSuite split.
Renamed TestSuite -> Suite.
Merge pull request #46 from fnothaft/collect-lengths

Collect transcript lengths prior to EM
[RNAdam-33] Implements the EM algorithm used in
Sailfish transcript quantification.
Merge pull request #47 from niranjan93/NK_EM_Algorithm

[RNAdam-33] Implements EM algorithm used in Sailfish transcript quantification.
Pulled Latest 11/25