Usage: chipscore [options] -A <feature A> -B <feature B> -b<from> -e<to> [-t <thres>] [<] <SGA file>
      - version 1.6.0
      where options are:
  		 -h          Show this help text
  		 -d          Print debug information and check SGA file
  		 -o          Oriented strand processing
  		 -r          Reverse extraction process
  		 -c <cutoff> Cutoff value for feature counts (default is 9999)
  		 -q          Report feature B tag counts as 'feature_name=<int>'

	Feature Extraction Tool for ChIP-seq data analysis.
	The program reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA file>),
	and compares two features, a reference feature (<feature A>) and a target feature
	(<feature B>), with respect to their relative position.
	By default, the program extracts feature A tags that are enriched in feature B
	tags according to a given count output threshold or score(<thres>) that is 0 by default.
	If option -r is specified, the program extracts sites that are depleted in feature B.
	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>.
	A value can be optionally specified as a cut-off for the feature counts.

