For example, what if you want the --length option to default to 10 when plotting but to 20 when calculating?

Solution a) Leave value undefined for now. (use topic-specific default value when you branch into that code)

my $opt_length;

GetOptions (
    "length=i" => \$opt_length, 
);

# call plot() or calc()

sub plot {
  my $length = opt_length // 10;

  ...
}

sub calc {
  my $length = opt_length // 20;

  ...
}
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Solution b) Only parse the first argument to decide which route to take and then hand over the rest of @ARGV to the next level -> http://perldoc.perl.org/Getopt/Long.html#Parsing-options-from-an-arbitrary-array