judy-dna.hs

import Data.List
import System.Environment (getArgs)
import Data.Maybe (fromMaybe)
import qualified Data.Judy as J
import qualified Data.ByteString as S
import Data.ByteString (ByteString)
import Control.Exception (evaluate)
import Data.Word

toWord = S.foldl' (\accum w -> accum * 4 + go w) 0
  where
    go 65 = 0
    go 67 = 1
    go 71 = 2
    go 84 = 3

update_freqM freq_delta j elem =
  do old <- J.lookup elem j
     J.insert elem ((fromMaybe (0::Int) old) + freq_delta) j

addTimesM freq_delta j l = mapM_ (update_freqM freq_delta j) l

timesM l = do j <- J.new
              addTimesM (1::Int) j l
              return j

kmers k l = map toWord . filter ((== k) . S.length) . map (S.take k) . S.tails $ l

main :: IO ()
main = do
    text <- S.getLine
    _l <- timesM . kmers 9 $ text
    return ()