CHANGES IN VERSION 1.2.5
-------------------------

BUG FIXES

    o Corrected a bug in the condition file name checking.
    o When using edgeR, it was not possible to de-activate
    the drawing of the quality assessment plots.
    o Some edgeR changes to the API have been ported to the
    stable R version, should not have occured... The following 
    are changes that adapt to that new API, changes ported from 
    version the easyRNASeq development version 1.3.3...
    o Adapted to the new arguments of the edgeR 
    estimateTagwiseDisp function
    o Removed the dispersion.method argument from the plotMeanVar
    edgeR method call as this argument is defunct.

CHANGES IN VERSION 1.2.4
-------------------------

    o Added the manuscript citation.
    o Updated the package version dependencies.

CHANGES IN VERSION 1.2.3
-------------------------

NEW FEATURES

    o Added an additional validity check for chromosome names
    Thanks to Simon Anders for generating a reproducible use-case for that.

    o Ensure that gtf with non Ensembl ID are correctly parsed as well.

CHANGES IN VERSION 1.2.2
-------------------------

BUG FIXES

    o Corrected a bug that was considering a GTF file as a GFF file.
    Thanks to Simon Anders for spotting this.

CHANGES IN VERSION 1.2.1
-------------------------

NEW FEATURES

    o Added an enhanced read length check

CHANGES IN VERSION 1.2.0
-------------------------

    o Stable version released as part of Bioconductor 2.10

CHANGES IN VERSION 1.1.10
-------------------------

NEW FEATURES

    o Added a naPositionFilter extending ShortRead srFilters

BUG FIXES

    o Worked on Wade Davis case with 3 different sets of chromosome
    names in the three different input (reads, annotation, chromosome
    sizes) 

    o Worked on smoother error handling when not using bam
    files. Again through Wade Davis example 

    o Ensured that chromosome names conversion occurs whether provided
    with a factor or a character vector 
    
    o extended the NAMESPACE

CHANGES IN VERSION 1.1.9
------------------------

BUG FIXES

    o Added an \alias{RNAseq} to ease the class documentation access;
    an H.Pages suggestion 

    o Changed the DESCRIPTION file to make sure that the latest
    ShortRead (1.13.13) and BiocGenerics (0.1.11) package are required 

CHANGES IN VERSION 1.1.8
------------------------

BUG FIXES

    o Corrected the last occurence of the deprecated matchMatrix call

    o Corrected an issue on windows raised by the parallel
    package. Thanks to Wade Davis for pointing that one out. 

CHANGES IN VERSION 1.1.7
------------------------

BUG FIXES

    o Fixed the NAMESPACE and the vignette generation

CHANGES IN VERSION 1.1.6
------------------------

BUG FIXES

    o Thanks to Francesco Lescai, a bug was fixed. Namely I was not
    expecting the chromosome names in the bam files and in the
    chromosome name lists to be two different set with a common
    intersect. I always consider that one would be the subset of the
    other one. Now, when such situation occurs only the common set is
    kept and used for the calculations. 

    o Herve Pages changed the findOverlaps value. It is now an object
    of the Hits class that does not support the matchMatrix accessor
    anymore. The code was adapted to the new accessor queryHits. 

    o Corrected the package structure to add a vignettes
    sub-directory. Moved the relevant files there 

CHANGES IN VERSION 1.1.5
------------------------

BUG FIXES

    o Removed the fitInfo method extension to the DESeq package as it
    as been implemented in that package 

    o Reworked the plotDispersionEstimates and
    .normalizationDispatcher function to deal with the new fitInfo
    function (the information is stored in an environment rather than
    in a list) 

CHANGES IN VERSION 1.1.4
------------------------

    o Package introduced in Bioconductor