...and one version based on regex if the number of switches is known:

use strict;
use warnings;

my $n_switches = 6;
while(<DATA>){
  my $last = 0;
  s/\s(\d+)/my $d = $1-$last-1; $last = $1; " 0"x$d." 1" /ge;
  s/\n/" 0" x ($n_switches-$last)."\n"/e;
  print;
}

__DATA__
run1 2 4
run2 1 6
run3 1
run4 1 3
run5 2 5
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