s|
    .*      # greedily match
    (\w)    # match first letter, and store into $1
    .*      # greedily match
    (\w)    # match last letter, and store into $2
    .*\n    # eat up remainder of line
  |
    # this expression maps the relevant character to its Base4 digit from 
    # the %_ hash. The $- is used as a line counter (it defaults to 0). When 
    # the DNA strands flip positions, this continues decoding on the correct
    # strand (see physi's comment for a visual representation of this)
    $_{$-++ / 9 % 2 ? $2:$ 1}
  |gex;