SuccessChanges

Summary

  1. Transition to Viterbi decking and normalized forward-backward (#32) (commit: 0e4a424854eb6206e4f4e6c907bad3ed53cab171) (details)
Commit 0e4a424854eb6206e4f4e6c907bad3ed53cab171 by heuermh
Transition to Viterbi decking and normalized forward-backward (#32)
* Add infrastructure and arguments to run on Amazon Elastic MapReduce

* Implement Viterbi decoding in discovery

* Integrate forward and Viterbi algorithms

* Test log space computations for Viterbi

* Transition to normalized calculations for forward-backward algorithm

* Fix bug in exact probability for single target events

* Update READMEs and other documentation

* Fix typos in documentation
(commit: 0e4a424854eb6206e4f4e6c907bad3ed53cab171)
The file was addeddeca-core/src/main/scala/org/bdgenomics/deca/hmm/FixedDoubleMatrix.scala
The file was modifiedpom.xml (diff)
The file was modifieddeca-core/src/main/scala/org/bdgenomics/deca/hmm/SampleModel.scala (diff)
The file was modifieddeca-core/src/main/scala/org/bdgenomics/deca/hmm/FixedVector.scala (diff)
The file was modifiedBENCHMARKING.md (diff)
The file was modifieddeca-core/src/main/scala/org/bdgenomics/deca/hmm/FixedMatrix.scala (diff)
The file was modifiedREADME.md (diff)
The file was modifieddeca-cli/src/main/scala/org/bdgenomics/deca/cli/NormalizingDiscoverer.scala (diff)
The file was modifieddeca-cli/src/main/scala/org/bdgenomics/deca/cli/Coverager.scala (diff)
The file was modifieddeca-core/src/main/scala/org/bdgenomics/deca/Timers.scala (diff)
The file was modifieddeca-cli/src/main/scala/org/bdgenomics/deca/cli/CNVer.scala (diff)
The file was modifieddeca-core/src/main/scala/org/bdgenomics/deca/hmm/TransitionProbabilities.scala (diff)
The file was modifieddeca-cli/src/main/scala/org/bdgenomics/deca/cli/Discoverer.scala (diff)
The file was modifieddeca-core/src/main/scala/org/bdgenomics/deca/Deca.scala (diff)
The file was modifiedscripts/hmm.R (diff)
The file was modifieddeca-core/src/main/scala/org/bdgenomics/deca/util/Phred.scala (diff)
The file was modifieddeca-core/src/test/scala/org/bdgenomics/deca/HMMSuite.scala (diff)
The file was modifieddeca-cli/src/main/scala/org/bdgenomics/deca/cli/Normalizer.scala (diff)
The file was addeddeca-core/src/main/scala/org/bdgenomics/deca/hmm/FixedDoubleVector.scala
The file was addedscripts/emr_config.json