Usage: bed2sga [options] [-s <s_assembly (e.g. hg19)>] [<] <BED file|stdin>
      - version 1.6.0
      where options are:
  		 -d|--debug                Produce Debug information
  		 -h|--help                 Show this Help text
  		 -i|--db <path>            Use <path> to locate the assembly-specific chr_NC_gi file
  		                           [default is current working directory]
  		 -f|--feature <ft>         Set Feature name <ft>
  		 -s|--species <spec>       Assembly <spec> (i.e hg19)
  		 -c|--center               Generate a Centered SGA file
  		 -u|--unoriented           Generate an unoriented SGA file
  		 -r|--regional             Generate a 2-line[+/-] SGA file representing BED regions
  		                           (e.g. RepeatMasker regions)
  		 -e|--extend <f1,f2,...>   Produce an extended SGA file with additional fields specified
  		                           by a comma-separated list of BED column numbers (from 1 to n)
  		 --useScore                Use the BED 'score' field (#5) to set the SGA 'count' field
  		 --useSigVal               Use the BED 'Signal Value' field (#7) to set the SGA 'count' field
  		                           [This option is only valid for ENCODE narrowPeak]
  		 --narrowPeak              Use this option for ENCODE narrowPeak format
  		                           [Options --useScore, -c, and -u are ignored]

	Convert BED format into SGA format.

