Repeated Code

The printout function now has two nearly identical branches

      26    sub printout {
      27      if ($ct_scanout ) {
      28        for ($i=0;$i<@{$chain[3]};$i++){
      29          for (@chain) { 
      30            next unless defined;
      31            $_->[$i] =~ s/0/L/g; 
      32            $_->[$i] =~ s/1/H/g;
      33          }
      34          my @chars = map $_->[$i], @chain;
      35          print OUTFILE "\n(ct_so\n", join("", @chars), "\n )";
      36        }
      37        $ct_scanout=0;
      38      } elsif ($ct_scanout==0) {
      39        for ($i=0;$i<@{$chain[3]};$i++) {
      40          for (@chain) {
      41            next unless defined;
      42            $_->[$i] =~ s/X/0/g;
      43          }
      44          my @chars = map $_->[$i], @chain;
      45          print OUTFILE "\n(ct_si  $ct_si{tdi}\n", join("", @chars), "\n )";
      46        }
      47      }
      48    }

We can (and should) see what happens if we merge them