{-|
  Rename reads in .SFF files to avoid name clashes.
  Apparently, reads with the same name crashes Newbler, and is
  in any case a bad idea.  This ensures uniqueness by appending a serial number to each read name in a set of files.
-}

module Main where

import Bio.Sequence.SFF
import System.Environment (getArgs)
import qualified Data.ByteString.Char8 as B

main :: IO ()
main = do
  fs <- getArgs
  if null fs then putStrLn "Usage: frename file1.sff [file2.sff ...]"
    else renameSFFs fs
         
renameSFFs :: [FilePath] -> IO ()
renameSFFs = go 0 
  where go _ [] = return ()
        go current (f:fs) = do
          (SFF h rs) <- readSFF f
          writeSFF ("r_"++f) (SFF h $ renameFrom current rs)
          go (current+num_reads h) fs
        renameFrom i rs = zipWith update [i..] rs
          where update j r = let h = read_header r
                                 rn = B.concat [read_name h, B.pack "_", B.pack (show j)]
                             in r { read_header = h { name_length = fromIntegral $ B.length rn, read_name = rn }}