\name{bsseqnews}
\title{bsseq news}
\encoding{UTF-8}
\section{Version 1.43.x}{
  \itemize{
    \item Fixed an issue with `collapseBSseq()` omitting an error.
    \item Deprecating `read.modkit()` and `read.modbam2bed()` in favor
      of `read.bedMethyl()`.
  }
}
\section{Version 1.43.x}{
  \itemize{
    \item Included text in the vignette on HDF5.
  }
}
\section{Version 1.41.x}{
  \itemize{
    \item Changing saveRDS to base::saveRDS following upstream changes.
  }
}
\section{Version 1.39.x}{
  \itemize{
    \item{Changing the default value of k in \code{BSmooth.tstat} from
      \code{k=101} to \code{k=21}.}
    \item{Removed \code{read.umtab}, \code{read.bsmooth}. The alignment
      program which produced these files have not been supported for
      years. }
    \item{Minor code and documentation chnages. Fixed usage of
      \code{class(x) == "y"} and added examples to some man pages.} 
    \item{\code{Bsseq()} is modified to store filtered matrix (ambigious
      modification status) for nanopore data.}
    \item{New function \code{read.modkit()} to read in methyl bed files
      generated from modkit and construct Bsseq objects. When there is
      no other modifications, one Bsseq object is constructed, and when
      there is other modification present, its methylation and
      corresponding coverage are also stored and two Bsseq objects are
      constructed. }  
    \item{New function \code{read.modbam2bed()} to read in, extract
      methylation, coverage and filtered data and create Bsseq object
      from methyl bed files obtained by modbam2bed. Some instructions
      for using modbam2bed is also provided.} 
  }
}


\section{Version 1.17.x}{
  \itemize{
    \item{\code{BSseq()} will no longer reorder inputs. Previously, the
      returned \emph{BSseq} object was ordered by ordering the loci, although
      this behaviour was not documented. \code{BSseq()} may still filter out loci
      if \code{rmZeroCov = FALSE} or collapse loci if
      \code{strandCollapse = FALSE} or duplicate loci are detected, but the
      relative order of loci in the output will match that of the input.
    }
    \item{Fix bug with \code{maxGap} argument of \code{BSmooth()}. The bug
      meant that the 'maximum gap between two methylation loci' was incorrectly
      set to \code{2 * maxGap + 1} instead of \code{maxGap}. This likely did not
      affect results for users who left the default value of \code{maxGap = 10^8}
      but may have affected results for small values of \code{maxGap}.
    }
    \item{Cleaning up Imports and Suggests.
    }
  }
}

\section{Version 1.13.x}{
  \itemize{
    \item{1.13.6: Fix performance regression in \code{BSmooth()}. Thanks to
    Shan Andrews for the report
    (\url{https://github.com/kasperdanielhansen/bsseq/pull/57}).}
    \item{1.13.5: Fix major bug in \code{combine()} and \code{combineList()}.
    \strong{This bug led to bad BSseq objects with incorrect methylation
    estimates due to incorrect 'M', 'Cov', 'coef', and 'se.coef' assays.} To be
    safe, BSseq objects created with versions 1.13.0 to 1.13.4 should be
    re-created using a newer version. More specifically, any BSseq objects
    created with \code{combine()} or \code{combineList()} should be re-created.
    Also, BSseq objects created using \code{read.bismark()} or
    \code{read.bsmooth()} with multiple '\code{files}' should be re-created.
    Thanks to Alejandro Reyes (@areyesq89) for the report
    (\url{https://github.com/kasperdanielhansen/bsseq/pull/54}).}
    \item{1.13.4: Fix performance regression in getMeth() and
    getCoverage() when '\code{regions}' were supplied. Thanks to Alejandro
    Reyes (@areyesq89) for the report
    (\url{https://support.bioconductor.org/p/97611/}).}
    \item Moved vignettes to Rmd.
  }
}



\section{Version 1.11.x}{
This version brings some new features for working with large
bisulfite-sequencing datasets. Adding these features has involved substantial
reworkings to the internals of bsseq. However, we have endeavoured to keep the
user-facing functionality unchanged. You will need to update old
serialized (saved) objects by invoking \code{x <- updateObject(x)}.

To support larger datasets, bsseq now provides the option of using disk-backed
BSseq, BSseqTstat, and BSseqStat objects. This can greatly reduce the memory
footprint when analysing large datasets. For example, the 'M', 'Cov', and
'coef' matrices in a BSseq object can be stored as HDF5 files on disk.

  \itemize{
    \item bsseq now uses DelayedMatrix objects from the DelayedArray package
    for all matrix-like data. This enables large data to be stored on disk
    rather than in memory.
    \item Serialized (saved) BSseq, BSseqTstat, and BSseqStat objects will need
    to be updated by invoking \code{x <- updateObject(x)}.
  }
}

\section{Version 1.7.x}{
  \itemize{
    \item Fixing an error with reading multiple samples aligned with
    bismark in the format "cytosineReport".
  }
}


\section{Version 1.5.x}{
  \itemize{
    \item new function strandCollapse for collapsing forward and reverse
    strand data to be unstranded.
    \item Updated read.bismark() to support the cytosine report files;
    both formats are supported. Other minor updates (mostly internal) to
    read.bismark(). Greatly improved documentation of this function, paying
    particular attention to differences in file formats between versions of
    Bismark.
  }
}

\section{Version 0.11.x}{
  \itemize{
    \item Converted to using Authors@R in the DESCRIPTION file.
    \item plotRegion did not respect the col/lty/lwd argument if given
    explicitely as opposed to through pData().  Reported by Karen
    Conneely <kconnee@emory.edu>.
    \item Fixed an issue introduced by the previous change (to
    plotRegion).  Reported (with a fix) by Tim Triche Jr
    <tim.triche@gmail.com>.
    \item Fixed a serious bug in collapseBSseq reported by Julien Roux
    <jroux@uchicago.edu>: it would use the Meth values instead of Cov
    for the final object's Cov.  However, this will result in the return
    object having a methylation of 100 percent across all loci, so
    hopefully users will have seen this for themselves.
    \item Fixed a bug in combineList which made combineList use "slow"
    code even in a special case where a faster shortcut was possible.
    This bug fix does not change the output of the function under any
    input, it only makes it faster.  Reported by Julien Roux
    <jroux@uchicago.edu>.
    \item validity now checks for the presence of colnames (sampleNames)
    which was assumed to be set.  Reported by Kevin Rue-Albrecht
    <kevin.rue@ucdconnect.ie>.
    \item Fixed a man page issue.
    \item Slightly changed CITATION.
    \item Added GitHub URL to DESCRIPTION.
  }
}

\section{Version 0.9.x}{
  \itemize{
    \item Fixed a problem with "width" in the title of bsseq plots.
    \item plot.BSseqTstat now allows for BSseqTstat objects computed
    without correction.
    \item validObject(BSseq) has been extended to also check for
    sampleNames consistency.
    \item Fixed a bug related to validity checking.
    \item Increased maxk from 10,000 to 50,000 in calls to locfit, to
    allowing fitting the model on genomes with unusally long chromosomes
    (Thanks to Brian Herb for reporting).
    \item The class representation for class 'BSseq' has changed
    completely. The new class is build on 'SummarizedExperiment' from
    GenomicRanges instead of 'hasGRanges'.  Use 'x <- updateObject(x)' to
    update serialized (saved) objects.
    \item Fixing a problem in orderBSseq related to chromosome names.
    \item Allowed user specification of maxk, with a default of 10,000
    in BSmooth.
    \item Many bugfixes made necessary by the new class representation.
    \item Better argument checking in BSmooth.tstat.
    \item A few undocumented functions are now documented.
    \item Rewrote orderBSseq
  }
}

\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.
  }
}

