Usage: chipcor [options] -A <feature A> -B <feature B> -b<from> -e<to> -w<window> [<] <SGA file>
       - version 1.6.0
       where options are:
  		 -h     Show this help text
  		 -d     Print debug information and check SGA file
  		 -c     Cut-Off value for feature counts (default is 1)
  		 -o     Oriented strand processing
  		 -n     Histogram Normalization (default is 0)

	Feature Correlation Tool for ChIP-seq data analysis.
	The program reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA file>),
	and generates histograms showing the positional relationship of two features,
	a reference feature (<feature A>) and a target feature (<feature B>) respectively.
	The feature specification must have the following format:
      	<feature> = <name> [<+|->]

	the strand specification (+|-) being optional.
	The <feature> parameter is a name that corresponds to the second field of the SGA file.
	If no feature is given then all input tags are processed.
	The SGA input file MUST BE sorted by sequence name (or chromosome id), position,
	and strand.
	One should check the input SGA file with the following command:
	sort -s -c -k1,1 -k3,3n -k4,4 <SGA file>.

	In debug mode (-d), the program performs the sorting order check.

	The relative distance between the two features is analysed within a
	given range: <from>-<to> that should be greater than 0.
	A value can be optionally specified as a cut-off for the feature counts.
	The window width (-w) defines the histogram step size or bin. It must be
	an integer greater than 0.
	For Histogram Normalization the following options are available:
  		   Off - Raw Counts (default)
  		   Show Count Density (-n 1)
  		   Show Global Normalization (-n 2)

