Usage: filter_counts [options] [<] <SGA File>
      - version 1.6.0
      where options are:
  		 -h     Show this help text
  		 -d     Print debug information
  		 -f     Feature defining the user-defined regions of interest (default=RMSK)
  		 -r     Retain Mode on

	The program reads a ChIP-seq data file (or from stdin [<]) in SGA format (<SGA File>)
	and filters out all read counts that occur within user-defined regions of interest, such
	as Repeat Mask regions (feature=RMSK).
	If 'Retain Mode' is on, it only retains those lines that are within the user-defined regions,
	in which case the annotation of the user-defined regions is added to the output SGA file.

