Note: Due to space limitations, the java source code has not been 
included with this package.  If you would like to obtain this code, 
please contact the package maintainer Chris Cabanski at ccabansk@dom.wustl.edu

September 4, 2012
-----------------
Our manuscript describing this package has been published in BMC Bioinformatics.
Refer to this paper for further description of the ReQON algorithm and a comparison 
with other quality score recalibration algorithms.  Please cite this paper if you
use our package.
    Cabanski CR et al. (2012) ReQON: a Bioconductor package for recalibrating quality 
    scores from next-generation sequencing data. BMC Bioinformatics 13(221). 
	doi:10.1186/1471-2105-13-221.


CHANGES in ReQON VERSION 1.2.0
-------------------------------

NEW FEATURES

	- Output BAM file keeps input header and adds header line:
		"@CO Quality scores were recalibrated with ReQON." 
	- Allow threshold options (nerr and nrf) to remove positions from
		the training set that are likely to contain incorrect error calls.
		(e.g., novel variants and systematic mapping errors)
	- diagnostic output now outputs flagged read positions ($FlagPos) and 
		regression coefficients ($coeff)
		
CHANGES in ReQON VERSION 1.3.2
-------------------------------

NEW FEATURES

	- ReQON no longer recalibrates 'N' bases.  It returns the original quality
		score for these bases in the output BAM file.
	- Minor modifications have been made to FWSEplot.R.  Points are now shaded
		according to the relative frequency of bases assigned that quality score.
		See the reference manual for more details.
		
CHANGES in ReQON VERSION 1.3.4
-------------------------------		

NEW FEATURES

	- An additional option has been added to ReadPosErrorPlot.R.  The option
		"startpos" now allows users to designate the starting read position to
		be plotted.  The default start position is 1.
	
BUG FIXES

	- The required version of R has increased to 2.15.  Major changes to the ReQON 
		package were made in version 1.2.0, and older versions of R would download
		ReQON v. 1.0.0, which is incompatible with the current documentation.
	- There were minor inconsistencies between the FWSE reported in the output 
		plots and FWSE calculated from the recalibrated BAM file, which has now
		been fixed.
		