[RNAdam-48] Added simple read simulator.
Merge pull request #49 from fnothaft/simple-sim

Adds simple read simulator
Changes were made to the m method in Quantify.scala so that the
"quantify unique transcripts" sparkTest in QuantifySuite.scala
passes. The problem was that in the m step of the EM algorithm,
the weight of equivalence class j for transcript i alpha_ji has
to be multiplied by the fraction of k-mers in equivalence class j.
The Sailfish paper (Patro et al., 2014) does not include this
in the EM algorithm equations it provides in the methods section.
Merge pull request #51 from niranjan93/Quantify.apply_unit_tests

Modification to EM algorithm
Merge remote-tracking branch 'upstream/master'