CHANGES IN VERSION 1.10.0 (2014-10-01)
--------------------------------------

NEW FEATURES
 o This release corresponds to C++ BitSeq version 0.7.5.
 o adding "unstranded" option to parseAlignment, to allow read pairs
   with various directions to be used
 o enable excluding singletons (single-mate alignments of paired reads)
   in parseAlignment

CHANGES IN VERSION 1.5.5 (2013-10-12)
-------------------------------------
BUG FIXES
  o fixed problem with processing Fasta reads
  o fixed problem with processing mixed alignments in empirical estimation
  o use proper includes for samtools
  
CHANGES IN VERSION 1.5.2  (2013-10-09)
-------------------------------------
BUG FIXES
  o fixed force option in estimateHyperPar (it worked the wrong way around)
  o fixed problem with effective lengths being too small

NEW FEATURES
  o add estimateVBExpression function that uses Variational Bayes inference
    method to estimate expression levels of transcripts

CHANGES IN VERSION 1.4.3  (2013-07-08)
-------------------------------------
BUG FIXES
  o fixed major bug in getGeneExpression and getWithinGeneExpression that
    caused wrong results for some genes if transcripts were not grouped by 
    genes

  o fixed bug in parseAlignment which would occasionally cause underflow in
    effective length computation

  o fixed taking square root of wrong column in getExpression result's $means
    field

NEW FEATURES
  o much faster parseAlignment computation

  o improved precision in getGeneExpression and getWithinGeneExpression

  o getWithinGeneExpression provides option to keep transcripts in original
    order even if they are not grouped by genes

CHANGES IN VERSION 1.3.11 (2013-04-02)
-------------------------------------
NEW FEATURES
  o new functions for handling transcript information

  o getExpression returns also counts and transcript information

CHANGES IN VERSION 1.3.10 (2013-03-30)
-------------------------------------
NEW FEATURES
  o proper handling of alignments from Bowtie2

CHANGES IN VERSION 1.3.6 (2013-03-19)
-------------------------------------
NEW FEATURES
  o enabling prallelization in getExpression via OpenMP
  
  o gene names can be extracted from Ensembl-like reference while estimating
    expression
  
  o added seed option for estimateHyperPar and estimateDE 
  
  o improved output for getDE when using more than 2 conditions
  
BUG FIXES
  o problem with long lines in reference sequence file in parseAlignment

CHANGES IN VERSION 1.2.2 (2013-01-29)
-------------------------------------
  o occasional crash when using non-uniform read model in getExpression

CHANGES IN VERSION 1.2.1 (2012-11-06)
-------------------------------------
  o parsing gapped alignments and half-alignments of paired end reads

CHANGES IN VERSION 1.2.0 (2012-09-27)
-------------------------------------
  o 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)

  o new internal structure (not visible to user)

  o estimateExpression has a new convergence criterion which should result in
    producing fewer samples. It is faster and avoids the use of
    MCMC_scaleReduction and MCMC_samplesNmax flags.

  o estimateExpressionLegacy uses the original convergence criterion

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

CHANGES IN VERSION 1.0.1 (2012-04-30)
-------------------------------------

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

  o improved manual, replaced overflowing lines

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


CHANGES IN VERSION 1.0.0 (2012-04-01)
-------------------------------------

  o First Bioconductor release of BitSeq
