Package: BitSeq
===============

Version 1.2.2 (29.1.2013)
- bug fix for getExpression which caused occasional crash when using non-uniform model

Version 1.2.1 (6.11.2012)
- bug fixes for parsing gapped alignments and half-alignments of paired end reads

Version: 1.2.0 (27.9.2012)
- IMPORTANT change: the way samples-files are passed to getDE, estimateHyperPar, estimateDE changed.
  -> instead of providing 2 vectors of filenames for each condition, the files are passed as a list
     of vectors, each vector containing filenames for one condition 
  (allowing use of more than 2 conditions)

- new internal structure (not visible to user)

- estimateExpression has a new convergence criterion which should result in producing fewer samples
  (faster and dropping the use of MCMC_scaleReduction and MCMC_samplesNmax flags)
  -> estimateExpressionLegacy uses the original convergence criterion

- library normalization option for getDE, estimateDE, estimateHyperPar, getMeanVariance
  (in form of providing the normalization constants, for getting the constants please use edgeR or 
   similar)

Version: 1.0.1 (30.4.2012)
Version: 1.1.1 (30.4.2012)

- fixed bug in estimateExpression (reading file with probabilities occasionally failed when 
  transcript information file was not specified) 

- improved manual, replaced overflowing lines

- added option "pretend" to produce C++ calls 


Version: 1.0.0

- First Bioconductor release of BitSeq
