\name{bsseqnews}
\title{bsseq news}
\encoding{UTF-8}

\section{Version 0.7.x}{
  \itemize{
    \item Removed the returnRaw argument to read.bismark() as it was
    unnecessary (Bismark output files does not have additional
    information beyond M and Cov and genomic positions, unlike BSmooth).
    \item Moved the Bismark example data from data to inst/extdata.
    \item combineList() now deals with the case where the list of BSseq
    objects have different genomic locations.  This speeds up
    read.bismark() substantially.
    \item Exposed combineList() as a faster alternative to
    Reduce(combine, list).
    \item Updated the code for the plotting routines (plotRegion).  This
    should not have an impact on user-visible code.
    \item Added read.bismark() function to parse output from the Bismark
    alignment suit [thanks to Pete Hickey].
    \item Refactorized plotting code.
  }
}

\section{Version 0.6.x}{
  \itemize{
    \item Fixed a bug in getMeth, where type="raw" resulted in an error
    for non-smoothed data objects.
    \item Updated CITATION and citations in the vignettes.
    \item Now read.bsmooth supports both gzipped and non-gzipped files,
    whereas previously it assumed the output files to be gzipped.
    Thanks to Andreas Schoenegger for reporting this problem.
    \item Fixed a bug in combine() that also resulted in a bug in
    read.bsmooth when multiple input directories were specified.  Bug
    reported by Andreas Schoenegger.
  }
}

\section{Version 0.4}{
  \itemize{
    \item Improved combine and fixed a bug.  Also added a non-exported
    combineList for testing.
    \item Bug fix to read.bsmooth; it now works correctly for the
    default settings (= returning a single object of class BSseq and not a
    list). 
    \item Getting ready for initial release on Bioconductor.
    \item Updated the citations in the vignette(s) and the CITATION file.
  }
}

