Usage: chippeak [options] [-f <feature>] -t <threshold> -w <window> -v <vicinity> [<] <SGA file>
      - version 1.6.0
      where options are:
  		 -h         Show this help text
  		 -d         Print debug information and check SGA file
  		 -i <dir>   Directory where the chr_size file is found
  		            [Default=/local/db/genome]
  		 -o         Oriented strand processing
  		 -r         Refine Peak Positions
  		 -c         Count Cut-off (default is 1)

	Locate signal peaks within SGA files.

	The program reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA file>),
	and detects signal peaks for ChIP-tag positions corresponding to a specific genomic
	feature (<feature>). The <feature> parameter is a name that corresponds to the second 
	field of the input SGA file. It might optionally include the strand specification (+|-).
	If no feature name is given then all input tags are processed.
	If the oriented option is specified (-o), peaks are separately detected on plus and minus
	strands, respectively.
	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.

	Additional input parameters are the integration range (<window>), the minimal distance
	amongst a group of high count local peaks (<vicinity>), and the peak threshold (<threshold>)
	whose default is 50. A value can be optionally specified as a cut-off for the feature counts.
	If peak refinement is required (-r option), the program recomputes the position of each
	peak by taking the center of gravity of the read counts within the peak region (<window>).
	The program also checks whether, after peak refinement, the new peak coordinates are still
	within chromosome boundaries. For that reason, the file chr_size must be read.
	The output is an SGA-formatted list containing signal peak locations.

