remove dependence on viterbi2Wrapper. Begin working on infrastructure for SummarizedExperiments
added tests
Add .gitignores
update to 1.9.01
merged with master branch
started to work on test_pipeline
Adding roxygen generated documentation
Add new Rd files
update .gitigore
Changes for R-devel. Fix infinite recursion error for GRanges objects by removing my own generic for ncol
Added MAP2 method for SnpArrayExperiment object
add defunct.R
update exports. Fix MAP2 unit test
add DNAcopyParam class
Add FileViews class, methods for FileViews, MinDistExperiment, and MinDistGRanges
Fixed bug in computing likelihood of first segment
Added methods-FileViews and others to index
changed default for minimum_emission from 1e-5 to 1e-9.  Change default for initial state probabilities to uniform
Compute posterior log odds for 221 or 220 states.  Compute posterior RR, posterior MAP and posterior 222
Fix bug in computePosteriorEmission