$CMD_LINE: Run script from a command line and retrieve the command line string (H)

• The global character variable $CMD_LINE is set to the command line string as reported by Windows when HicEst is started from a command line.
• Use $CMD_LINE as any other string to control your script
• "RUN=" somewhere in $CMD_LINE to

  start HicEst in run mode

  • "c:\...\HicEst.exe yourscript.hic RUN= XYZ=3.14 ALFA="some string"
  This will make $CMD_LINE available as a global variable in yourscipt.hic.
• Try the INIT() function to

  set variables from command line

  • INIT($CMD_LINE, alfa, xyz)
  • ! will set xyz to 3.14 and alfa to "some string"
• To close HicEst from within the script use ALARM()
  • ALARM(999) will immediately close HicEst

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