bigdatagenomics/RNAdam — pull request #51 by niranjan93 (2014-12-11 22:26:04+00:00)
Title: Modification to EM algorithm

See pull request #49
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.