-- main function for using single-threaded arrays
-- providing a baseline for performance

import System.Environment (getArgs)
import Data.Array.IO

import Base
import Cluster
import ContigEnds

main :: IO ()
main = do
  [bam] <- getArgs -- use a single bam file
  timestamp "start"
  (n,ls,rds) <- collect_links bam
  timestamp "links collected"  
  as <- initializeIO n
  timestamp "initialized"
  mapM_ (scaffold1 rds ls as) [0..n-1]  
  timestamp "scaffolded"
  printIO (snd as)
  timestamp "done!"