Usage: chipextract [options] -A <feature A> -B <feature B> -b <from> -e <to> -w <width> [<] <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 target feature counts (default is 1)

	Feature Correlation and Extraction Tool for ChIP-seq data analysis.
	The program reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA file>),
	containing two features, a reference feature (<feature A>) and a target feature (<feature B>),
	correlates the genomic tag count distributions for the two features, and for each reference 
	feature, it extracts target feature tags that fall into a distance range ([from,to]) relative
	to the reference feature.
	The feature specification must have the following format:
      	<feature> = <name> [<+|-|0[strandless]|a[any]|o[oriented]>]

	meaning that the feature field has a name and a strand specification.
	Accepted strand values are the following: +|-|0[strandless]|a[any]|o[oriented].
	If the strand is not specified, it is set to a[any] by default.
	The <feature> name corresponds to the second field of the SGA file.
	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 cut-off value may be specified for the target feature counts.
	The window width (-w) defines the histogram step size or bin. It must be an integer greater than 0.
	The output is a table in text format consisting of all reference features (rows) with relative
	target tag counts in bins of a given size defined by window width (-w<bin>) (columns).

