varan-0.5: src/Options.hs

{-# Language DeriveDataTypeable #-}

module Options (Options(..), getArgs) where

import System.Console.CmdArgs
import qualified Data.ByteString.Lazy.Char8 as BL
import System.IO

-- data SnpMode = Default | Pairwise | Groups deriving (Typeable,Data)

data Options = Opts 
  { suppress, variants
  , chi2, f_st, pi_k
  , conf, ds, dsw, esi, pconf, nd_all, maf  :: Bool
  , input, output :: FilePath
  , global :: Bool
  , threads :: Int
  , min_cov, max_cov :: Int
  } deriving (Typeable,Data)

defopts :: Options
defopts = Opts 
  { 
  -- General parameters
    output = "" &= help "output file name" &= typFile
  , suppress = False &= help "omit non-variant lines from output"
  , variants = False &= help "output list of non-SNP variants"
  , threads = 100 &= help "queue lenght for parallel execution"
  , min_cov = 0     &= help "minimum coverage to include"
  , max_cov = 32000 &= help "maximum coverage to include"
  , input  = [] &= args &= typFile
  
  , global = False &= help "calculate global statistics"

  -- Overall statistics
  , chi2   = False &= help "calculate chi² probability" &= ignore
  , f_st   = False &= help "estimate fixation index, F_st" &= name "fst"
  , pi_k   = False &= help "estimate nucleotide diversity, Pi_k"

  -- Per sample statistics (vs. pool of all populations)
  , conf   = False &= help "check if major allele frequency confidence intervals overlap" -- uses conf_all (for each allele)
  , pconf  = False &= help "pairwise major allele confidence"                             -- uses dsconf_pairs (by major allele)
  , ds     = False &= help "distance between major allele frequency confidence intervals, using Agresti-Coull" -- uses ds_all (by major allele)
  , dsw    = False &= help "lower bound for distance between major allele frequencies, using Wald"
  , nd_all = False &= help "nucleotide diversity (unadjusted), per sample and overall"
  , maf    = False &= help "minor allele frequency per position"

  -- Statistics for all sample pairs
  , esi    = False &= help "output conservative expected site information for SNPs using Agresti-Coull intervals"
  }
  &= program "varan v0.5"
  &= summary "Identify genetic variants from pooled sequences."
  &= details ["Examples:", ""
             ,"Read input from a pipe, calculate site-wise Fst and confidence intervals, ignoring non-variant sites:"
             ,"", "  samtools mpileup -f ref.fasta reads.bam | varan --fst --conf -s -o snps.txt", ""
             ,"Read input from a file, send the site-wise output to /dev/null, and only output global statistics to standard output:"
             ,"", "  varan --global -o /dev/null input.mpile", ""
             ,"If you use this program, please cite:"
             ,"  BMC Genomics 2014, 15(Suppl 6):S20"
             ,"  http://www.biomedcentral.com/1471-2164/15/S6/S20"
               ]    

getArgs :: IO (IO BL.ByteString,Options)
getArgs = do
  opts <- cmdArgs defopts
  inp  <- get_input opts
  return (inp,opts)
  
-- | Determine where and how to read the input mpile data.
get_input :: Options -> IO (IO BL.ByteString)
get_input o = do
  interactive <- hIsTerminalDevice stdin
  return $ if null (input o) then 
             if interactive then error "Cowardly refusing to read input from terminal.\nIf you really want this, specify '-' as input.\n(or use --help for help)."
             else BL.getContents
           else if input o == "-" then BL.getContents 
                else BL.readFile (input o)