Usage: chippart [options] [-f <feature>] -s <densitiy threshold> -p <transition penalty> [<] <SGA file>
      - version 1.6.0
      where options are:
  		 -h          Show this help text
  		 -d          Print debug information and check SGA file
  		 -c <cutoff> Count Cut-off (default is 1). It must be >= 0.

	Partitioning Tool.

	The program reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA file>),
	and heuristically partitions the data corresponding to a specific feature
	<feature>, if the latter is given.
	The <feature> parameter is a name that corresponds to the second field of the SGA file.
	It might optionally include the strand specification (+|-).
	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.

	Input parameters are the density threshold (<density threshold>),
	the transition penalty (<transition penalty>), which are used to
	split the data in regions of high density count.
	A value can be optionally specified as a cut-off for the feature counts.
	The output is an SGA-formatted list containing the regions of interest.
	The program also generates (to stderr) a statistical report with the
	following information:
	  - Total number of processed sequences, total DNA length, and
	    total number of fragments;
	  - Total length of fragments, average fragment length, and
	    percentage of total DNA length;
	  - Percentage of total counts, average number of counts, and
	    number of count per bp (count density).

