`cleanup`

      sub cleanup {
        s/^\s+|\s*\n+$//g;
        tr/\t  //d;            
        s/\n//g;                
        s/\\//g;
      }

The input looks like:

             chain "chain1" =
     "00110011001100110011001100110011001100110011001100\

     11001100110011001100110011001100110011001100110011\

     00110011001100110011001100110011001100110011001100\
        ...
     00110011001100110011001100110011001100110011001100\
                           1100110011001100110011001100110011001100110"

The output should be an array of just the 0s and 1s

        sub cleanup {
          my $i = shift;
          my ($bits) =   $i =~ /=\s*"(.*)"/m;
          $bits =~ tr/01//cd;
          return [ split //, $bits ]
        }