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.
[RNAdam-48] Added simple read simulator.