qrqc -- history of changes.

Copyright (c) Vince Buffalo 2011-2012

Version 1.9.1: (2012-02-20)

 - plotQuals, plotBase, plotSeqLengths, plotGC replaced by qualPlot,
   basePlot, seqlenPlot, and gcPlot, respectively. These should be
   used for all plotting; these other functions are now
   deprecated. These new methods are all based on ggplot2.

   These new plotting functions now have methods for a named list of
   SequencySummary objects, which can be useful in comparing many
   sequence files at once.

 - There are also helper plotting functions scale_color_dna,
   scale_color_iupac, and geom_qlinerange for creating plots.

 - reportMethods now uses these new plotting methods.

 - New accessor functions getBase, getBaseProp, getQual, getSeqlen,
   and getMCQual can be used to return data frames of data from
   SequencySummary object.

 - Added function list2df for applying a function to objects in a
   named list and combining the results into a data frame. This is
   used in graphing lists of SequencySummary objects.

 - Removed Phred quality as a visible option in readSeqFile. I don't
   believe this should affect any users, but if it does, let me know.