{-| FlowClip reads in an SFF file using coordinates provided on the
    command line, and clips each read accordingly.  Negative coordinates
    indicate counting from the left, so to clip the last 20 bases off
    each read (useful for removing adapters), do 'flowclip 0 -20 input.sff'.
-}

module Main where

import Bio.Sequence.SFF
import System.Environment (getArgs)
import Data.Int

main :: IO ()
main = do
  [from,to,input] <- getArgs
  SFF h rs <- readSFF input
  writeSFF (input++".clip") (SFF h $ map (clip (read from) (read to)) rs)
  
clip :: Int32 -> Int32 -> ReadBlock -> ReadBlock
clip f t rb = let 
  rh    = read_header rb
  n     = num_bases rh
  left  = if f < 0 then n+f else f
  right = if t < 0 then n+t else t
  in trimFromTo left right rb